-- dump date 20140618_185648 -- class Genbank::misc_feature -- table misc_feature_note -- id note 358220000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 358220000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 358220000003 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220000004 Walker A motif; other site 358220000005 ATP binding site [chemical binding]; other site 358220000006 Walker B motif; other site 358220000007 arginine finger; other site 358220000008 C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple...; Region: Bac_DnaA_C; cd06571 358220000009 DnaA box-binding interface [nucleotide binding]; other site 358220000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 358220000011 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 358220000012 putative DNA binding surface [nucleotide binding]; other site 358220000013 dimer interface [polypeptide binding]; other site 358220000014 beta-clamp/clamp loader binding surface; other site 358220000015 beta-clamp/translesion DNA polymerase binding surface; other site 358220000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 358220000017 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220000018 ATP binding site [chemical binding]; other site 358220000019 Mg2+ binding site [ion binding]; other site 358220000020 G-X-G motif; other site 358220000021 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 358220000022 anchoring element; other site 358220000023 dimer interface [polypeptide binding]; other site 358220000024 ATP binding site [chemical binding]; other site 358220000025 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 358220000026 active site 358220000027 putative metal-binding site [ion binding]; other site 358220000028 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 358220000029 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 358220000030 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 358220000031 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 358220000032 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 358220000033 acyl-activating enzyme (AAE) consensus motif; other site 358220000034 putative AMP binding site [chemical binding]; other site 358220000035 putative active site [active] 358220000036 putative CoA binding site [chemical binding]; other site 358220000037 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 358220000038 Beta-lactamase; Region: Beta-lactamase; pfam00144 358220000039 TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA...; Region: TlpA_like_DipZ_like; cd03012 358220000040 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 358220000041 catalytic residues [active] 358220000042 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 358220000043 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 358220000044 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 358220000045 osmolarity response regulator; Provisional; Region: ompR; PRK09468 358220000046 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220000047 active site 358220000048 phosphorylation site [posttranslational modification] 358220000049 intermolecular recognition site; other site 358220000050 dimerization interface [polypeptide binding]; other site 358220000051 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220000052 DNA binding site [nucleotide binding] 358220000053 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 358220000054 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220000055 ATP binding site [chemical binding]; other site 358220000056 Mg2+ binding site [ion binding]; other site 358220000057 G-X-G motif; other site 358220000058 Acylphosphatase; Region: Acylphosphatase; pfam00708 358220000059 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 358220000060 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 358220000061 homoserine dehydrogenase; Provisional; Region: PRK06349 358220000062 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 358220000063 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 358220000064 Transcriptional regulator [Transcription]; Region: PaiB; COG2808 358220000065 OsmC-like protein; Region: OsmC; cl00767 358220000066 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 358220000067 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220000068 DNA-binding site [nucleotide binding]; DNA binding site 358220000069 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220000070 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220000071 homodimer interface [polypeptide binding]; other site 358220000072 catalytic residue [active] 358220000073 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 358220000074 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 358220000075 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220000076 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220000077 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 358220000078 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 358220000079 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 358220000080 trimer interface [polypeptide binding]; other site 358220000081 putative metal binding site [ion binding]; other site 358220000082 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220000083 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 358220000084 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220000085 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220000086 metal binding site [ion binding]; metal-binding site 358220000087 active site 358220000088 I-site; other site 358220000089 B12 binding domain; Region: B12-binding; pfam02310 358220000090 B12 binding site [chemical binding]; other site 358220000091 Radical SAM superfamily; Region: Radical_SAM; pfam04055 358220000092 N-acetylmuramoyl-L-alanine amidase; Region: Amidase_2; pfam01510 358220000093 amidase catalytic site [active] 358220000094 Zn binding residues [ion binding]; other site 358220000095 substrate binding site [chemical binding]; other site 358220000096 Integrase core domain; Region: rve; pfam00665 358220000097 Integrase core domain; Region: rve_3; pfam13683 358220000098 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 358220000099 DEAD_2; Region: DEAD_2; pfam06733 358220000100 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 358220000101 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 358220000102 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 358220000103 PhnA protein; Region: PhnA; pfam03831 358220000104 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 358220000105 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 358220000106 Beta-lactamase; Region: Beta-lactamase; pfam00144 358220000107 D-aminopeptidase; Reviewed; Region: PRK13128 358220000108 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 358220000109 active site 358220000110 catalytic site [active] 358220000111 substrate binding site [chemical binding]; other site 358220000112 NnrU protein; Region: NnrU; pfam07298 358220000113 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 358220000114 RNAse HI family that includes Archaeal RNase HI; Region: RNase_HI_archaeal_like; cd09279 358220000115 active site 358220000116 RNA/DNA hybrid binding site [nucleotide binding]; other site 358220000117 Uncharacterized conserved protein [Function unknown]; Region: COG3791 358220000118 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 358220000119 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220000120 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_24; cd09012 358220000121 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_1; cd07818 358220000122 putative hydrophobic ligand binding site [chemical binding]; other site 358220000123 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3795 358220000124 YCII-related domain; Region: YCII; cl00999 358220000125 2-isopropylmalate synthase; Validated; Region: PRK03739 358220000126 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 358220000127 active site 358220000128 catalytic residues [active] 358220000129 metal binding site [ion binding]; metal-binding site 358220000130 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 358220000131 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 358220000132 NlpC/P60 family; Region: NLPC_P60; pfam00877 358220000133 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 358220000134 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 358220000135 eyelet of channel; other site 358220000136 trimer interface [polypeptide binding]; other site 358220000137 protocatechuate 4,5-dioxygenase; Provisional; Region: PRK13367 358220000138 The N-terminal domain of the Class III extradiol dioxygenase, Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate; Region: Gallate_Doxase_N; cd07950 358220000139 putative active site [active] 358220000140 Fe(II) binding site [ion binding]; other site 358220000141 putative dimer interface [polypeptide binding]; other site 358220000142 The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate; Region: Gallate_dioxygenase_C; cd07923 358220000143 putative dimer interface [polypeptide binding]; other site 358220000144 putative N- and C-terminal domain interface [polypeptide binding]; other site 358220000145 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 358220000146 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220000147 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 358220000148 DctM-like transporters; Region: DctM; pfam06808 358220000149 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 358220000150 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 358220000151 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220000152 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000153 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220000154 dimerization interface [polypeptide binding]; other site 358220000155 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 358220000156 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 358220000157 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220000158 CoenzymeA binding site [chemical binding]; other site 358220000159 subunit interaction site [polypeptide binding]; other site 358220000160 PHB binding site; other site 358220000161 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 358220000162 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 358220000163 DNA binding residues [nucleotide binding] 358220000164 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220000165 GAF domain; Region: GAF; pfam01590 358220000166 PAS fold; Region: PAS_3; pfam08447 358220000167 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220000168 putative active site [active] 358220000169 heme pocket [chemical binding]; other site 358220000170 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220000171 PAS fold; Region: PAS_3; pfam08447 358220000172 putative active site [active] 358220000173 heme pocket [chemical binding]; other site 358220000174 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220000175 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 358220000176 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220000177 putative active site [active] 358220000178 heme pocket [chemical binding]; other site 358220000179 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220000180 GAF domain; Region: GAF; pfam01590 358220000181 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220000182 PAS domain; Region: PAS_9; pfam13426 358220000183 putative active site [active] 358220000184 heme pocket [chemical binding]; other site 358220000185 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220000186 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220000187 metal binding site [ion binding]; metal-binding site 358220000188 active site 358220000189 I-site; other site 358220000190 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220000191 LTXXQ motif family protein; Region: LTXXQ; pfam07813 358220000192 recombination associated protein; Reviewed; Region: rdgC; PRK00321 358220000193 Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]; Region: ChaC; COG3703 358220000194 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 358220000195 putative active site pocket [active] 358220000196 dimerization interface [polypeptide binding]; other site 358220000197 putative catalytic residue [active] 358220000198 Pirin-related protein [General function prediction only]; Region: COG1741 358220000199 Pirin; Region: Pirin; pfam02678 358220000200 enoyl-CoA hydratase; Provisional; Region: PRK06688 358220000201 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220000202 substrate binding site [chemical binding]; other site 358220000203 oxyanion hole (OAH) forming residues; other site 358220000204 trimer interface [polypeptide binding]; other site 358220000205 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 358220000206 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220000207 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 358220000208 acyl-activating enzyme (AAE) consensus motif; other site 358220000209 putative AMP binding site [chemical binding]; other site 358220000210 putative active site [active] 358220000211 putative CoA binding site [chemical binding]; other site 358220000212 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220000213 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220000214 Walker A/P-loop; other site 358220000215 ATP binding site [chemical binding]; other site 358220000216 Q-loop/lid; other site 358220000217 ABC transporter signature motif; other site 358220000218 Walker B; other site 358220000219 D-loop; other site 358220000220 H-loop/switch region; other site 358220000221 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220000222 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 358220000223 putative ligand binding site [chemical binding]; other site 358220000224 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220000225 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220000226 TM-ABC transporter signature motif; other site 358220000227 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220000228 TM-ABC transporter signature motif; other site 358220000229 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220000230 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220000231 Walker A/P-loop; other site 358220000232 ATP binding site [chemical binding]; other site 358220000233 Q-loop/lid; other site 358220000234 ABC transporter signature motif; other site 358220000235 Walker B; other site 358220000236 D-loop; other site 358220000237 H-loop/switch region; other site 358220000238 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220000239 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220000240 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 358220000241 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 358220000242 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 358220000243 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220000244 ATP binding site [chemical binding]; other site 358220000245 putative Mg++ binding site [ion binding]; other site 358220000246 nucleotide binding region [chemical binding]; other site 358220000247 Helicase conserved C-terminal domain; Region: Helicase_C; pfam00271 358220000248 ATP-binding site [chemical binding]; other site 358220000249 HipA N-terminal domain; Region: Couple_hipA; pfam13657 358220000250 HipA-like N-terminal domain; Region: HipA_N; pfam07805 358220000251 HipA-like C-terminal domain; Region: HipA_C; pfam07804 358220000252 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220000253 non-specific DNA binding site [nucleotide binding]; other site 358220000254 salt bridge; other site 358220000255 sequence-specific DNA binding site [nucleotide binding]; other site 358220000256 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4634 358220000257 Protein of unknown function (DUF433); Region: DUF433; pfam04255 358220000258 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 358220000259 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 358220000260 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 358220000261 HsdM N-terminal domain; Region: HsdM_N; pfam12161 358220000262 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 358220000263 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 358220000264 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 358220000265 DNA binding residues [nucleotide binding] 358220000266 dimer interface [polypeptide binding]; other site 358220000267 copper binding site [ion binding]; other site 358220000268 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220000269 metal-binding site [ion binding] 358220000270 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 358220000271 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220000272 metal-binding site [ion binding] 358220000273 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220000274 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220000275 motif II; other site 358220000276 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220000277 dimerization interface [polypeptide binding]; other site 358220000278 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220000279 dimer interface [polypeptide binding]; other site 358220000280 putative CheW interface [polypeptide binding]; other site 358220000281 Hemerythrin-like domain; Region: Hr-like; cd12108 358220000282 Fe binding site [ion binding]; other site 358220000283 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 358220000284 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 358220000285 FMN binding site [chemical binding]; other site 358220000286 active site 358220000287 substrate binding site [chemical binding]; other site 358220000288 catalytic residue [active] 358220000289 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 358220000290 glutathionine S-transferase; Provisional; Region: PRK10542 358220000291 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 358220000292 C-terminal domain interface [polypeptide binding]; other site 358220000293 GSH binding site (G-site) [chemical binding]; other site 358220000294 dimer interface [polypeptide binding]; other site 358220000295 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 358220000296 dimer interface [polypeptide binding]; other site 358220000297 N-terminal domain interface [polypeptide binding]; other site 358220000298 substrate binding pocket (H-site) [chemical binding]; other site 358220000299 aldolase II superfamily protein; Provisional; Region: PRK07044 358220000300 intersubunit interface [polypeptide binding]; other site 358220000301 active site 358220000302 Zn2+ binding site [ion binding]; other site 358220000303 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 358220000304 Uncharacterized conserved protein [Function unknown]; Region: COG2128 358220000305 RNA polymerase sigma-70 factor, TIGR02957 family; Region: SigX4 358220000306 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220000307 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220000308 DNA binding residues [nucleotide binding] 358220000309 Flagellin N-methylase; Region: FliB; pfam03692 358220000310 Predicted flavoprotein [General function prediction only]; Region: COG0431 358220000311 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 358220000312 potential frameshift: common BLAST hit: gi|222109270|ref|YP_002551534.1| tRNA uridine 5-carboxymethylaminomethyl modification protein GidA 358220000313 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 358220000314 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 358220000315 LysE type translocator; Region: LysE; cl00565 358220000316 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 358220000317 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 358220000318 P-loop; other site 358220000319 Magnesium ion binding site [ion binding]; other site 358220000320 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 358220000321 Magnesium ion binding site [ion binding]; other site 358220000322 Serine hydrolase; Region: Ser_hydrolase; pfam06821 358220000323 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220000324 Cupin domain; Region: Cupin_2; pfam07883 358220000325 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 358220000326 ParB-like nuclease domain; Region: ParB; smart00470 358220000327 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 358220000328 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 358220000329 putative dimer interface [polypeptide binding]; other site 358220000330 Protein of unknown function (DUF3897); Region: DUF3897; pfam13036 358220000331 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 358220000332 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 358220000333 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 358220000334 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220000335 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220000336 putative substrate translocation pore; other site 358220000337 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 358220000338 putative transposase OrfB; Reviewed; Region: PHA02517 358220000339 Integrase core domain; Region: rve; pfam00665 358220000340 Integrase core domain; Region: rve_3; pfam13683 358220000341 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220000342 Homeodomain-like domain; Region: HTH_23; cl17451 358220000343 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 358220000344 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 358220000345 metallophosphoesterase, DNA ligase-associated; Region: P_estr_lig_assc; TIGR04123 358220000346 active site 358220000347 metal binding site [ion binding]; metal-binding site 358220000348 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 358220000349 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220000350 ATP binding site [chemical binding]; other site 358220000351 putative Mg++ binding site [ion binding]; other site 358220000352 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220000353 nucleotide binding region [chemical binding]; other site 358220000354 ATP-binding site [chemical binding]; other site 358220000355 DEAD/H associated; Region: DEAD_assoc; pfam08494 358220000356 ATP-dependent DNA ligase; Validated; Region: PRK09247 358220000357 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 358220000358 active site 358220000359 DNA binding site [nucleotide binding] 358220000360 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 358220000361 DNA binding site [nucleotide binding] 358220000362 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 358220000363 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 358220000364 BON domain; Region: BON; pfam04972 358220000365 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 358220000366 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 358220000367 hypothetical protein; Provisional; Region: PRK02237 358220000368 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220000369 dimerization interface [polypeptide binding]; other site 358220000370 putative DNA binding site [nucleotide binding]; other site 358220000371 Transcriptional regulators [Transcription]; Region: MarR; COG1846 358220000372 putative Zn2+ binding site [ion binding]; other site 358220000373 NIPSNAP; Region: NIPSNAP; pfam07978 358220000374 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 358220000375 Domain of unknown function (DUF4259); Region: DUF4259; pfam14078 358220000376 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 358220000377 FAD binding domain; Region: FAD_binding_4; pfam01565 358220000378 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220000379 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220000380 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220000381 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 358220000382 Carboxylesterase family; Region: COesterase; pfam00135 358220000383 substrate binding pocket [chemical binding]; other site 358220000384 catalytic triad [active] 358220000385 Protein of unknown function (DUF2752); Region: DUF2752; pfam10825 358220000386 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220000387 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220000388 DNA-binding site [nucleotide binding]; DNA binding site 358220000389 FCD domain; Region: FCD; pfam07729 358220000390 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220000391 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220000392 substrate binding pocket [chemical binding]; other site 358220000393 membrane-bound complex binding site; other site 358220000394 hinge residues; other site 358220000395 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220000396 dimer interface [polypeptide binding]; other site 358220000397 conserved gate region; other site 358220000398 putative PBP binding loops; other site 358220000399 ABC-ATPase subunit interface; other site 358220000400 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 358220000401 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220000402 dimer interface [polypeptide binding]; other site 358220000403 conserved gate region; other site 358220000404 putative PBP binding loops; other site 358220000405 ABC-ATPase subunit interface; other site 358220000406 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 358220000407 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 358220000408 Walker A/P-loop; other site 358220000409 ATP binding site [chemical binding]; other site 358220000410 Q-loop/lid; other site 358220000411 ABC transporter signature motif; other site 358220000412 Walker B; other site 358220000413 D-loop; other site 358220000414 H-loop/switch region; other site 358220000415 EF-hand domain pair; Region: EF_hand_5; pfam13499 358220000416 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 358220000417 Ca2+ binding site [ion binding]; other site 358220000418 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 358220000419 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 358220000420 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220000421 CoenzymeA binding site [chemical binding]; other site 358220000422 subunit interaction site [polypeptide binding]; other site 358220000423 PHB binding site; other site 358220000424 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220000425 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220000426 putative ligand binding site [chemical binding]; other site 358220000427 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 358220000428 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 358220000429 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 358220000430 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 358220000431 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 358220000432 Transcription factor zinc-finger; Region: zf-TFIIB; cl01565 358220000433 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3315 358220000434 Leucine carboxyl methyltransferase; Region: LCM; pfam04072 358220000435 hypothetical protein; Provisional; Region: PRK09126 358220000436 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220000437 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220000438 Helix-turn-helix domain; Region: HTH_38; pfam13936 358220000439 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220000440 Integrase core domain; Region: rve; pfam00665 358220000441 BCCT family transporter; Region: BCCT; pfam02028 358220000442 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 358220000443 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 358220000444 acyl-activating enzyme (AAE) consensus motif; other site 358220000445 putative AMP binding site [chemical binding]; other site 358220000446 putative active site [active] 358220000447 putative CoA binding site [chemical binding]; other site 358220000448 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220000449 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 358220000450 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220000451 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_4; cd05944 358220000452 acyl-activating enzyme (AAE) consensus motif; other site 358220000453 putative AMP binding site [chemical binding]; other site 358220000454 putative active site [active] 358220000455 putative CoA binding site [chemical binding]; other site 358220000456 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 358220000457 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 358220000458 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 358220000459 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220000460 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000461 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 358220000462 dimerization interface [polypeptide binding]; other site 358220000463 substrate binding pocket [chemical binding]; other site 358220000464 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220000465 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220000466 metal binding site [ion binding]; metal-binding site 358220000467 active site 358220000468 I-site; other site 358220000469 EamA-like transporter family; Region: EamA; pfam00892 358220000470 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220000471 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 358220000472 Septum formation inhibitor [Cell division and chromosome partitioning]; Region: MinC; COG0850 358220000473 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 358220000474 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 358220000475 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 358220000476 Switch I; other site 358220000477 Switch II; other site 358220000478 cell division topological specificity factor MinE; Provisional; Region: PRK13989 358220000479 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 358220000480 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 358220000481 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 358220000482 MOSC domain; Region: MOSC; pfam03473 358220000483 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 358220000484 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220000485 Uncharacterized conserved protein [Function unknown]; Region: COG1434 358220000486 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 358220000487 putative active site [active] 358220000488 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 358220000489 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 358220000490 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 358220000491 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 358220000492 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 358220000493 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000494 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220000495 dimerization interface [polypeptide binding]; other site 358220000496 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220000497 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220000498 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 358220000499 Fasciclin domain; Region: Fasciclin; pfam02469 358220000500 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 358220000501 Fasciclin domain; Region: Fasciclin; pfam02469 358220000502 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 358220000503 Fasciclin domain; Region: Fasciclin; pfam02469 358220000504 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 358220000505 Ligand Binding Site [chemical binding]; other site 358220000506 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 358220000507 active site 358220000508 metal binding site [ion binding]; metal-binding site 358220000509 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220000510 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000511 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 358220000512 substrate binding pocket [chemical binding]; other site 358220000513 dimerization interface [polypeptide binding]; other site 358220000514 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_GTP; cd00819 358220000515 active site 358220000516 substrate-binding site [chemical binding]; other site 358220000517 metal-binding site [ion binding] 358220000518 GTP binding site [chemical binding]; other site 358220000519 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 358220000520 Ligand Binding Site [chemical binding]; other site 358220000521 threonine dehydratase; Provisional; Region: PRK07334 358220000522 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 358220000523 tetramer interface [polypeptide binding]; other site 358220000524 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220000525 catalytic residue [active] 358220000526 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 358220000527 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 358220000528 GAF domain; Region: GAF; pfam01590 358220000529 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220000530 Walker A motif; other site 358220000531 ATP binding site [chemical binding]; other site 358220000532 Walker B motif; other site 358220000533 arginine finger; other site 358220000534 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 358220000535 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 358220000536 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 358220000537 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220000538 ATP binding site [chemical binding]; other site 358220000539 putative Mg++ binding site [ion binding]; other site 358220000540 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220000541 nucleotide binding region [chemical binding]; other site 358220000542 ATP-binding site [chemical binding]; other site 358220000543 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 358220000544 HRDC domain; Region: HRDC; pfam00570 358220000545 potential frameshift: common BLAST hit: gi|333914782|ref|YP_004488514.1| RNP-1 like RNA-binding protein 358220000546 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220000547 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 358220000548 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 358220000549 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 358220000550 DctM-like transporters; Region: DctM; pfam06808 358220000551 D-lactate dehydrogenase; Provisional; Region: PRK11183 358220000552 FAD binding domain; Region: FAD_binding_4; pfam01565 358220000553 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 358220000554 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 358220000555 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 358220000556 dimer interface [polypeptide binding]; other site 358220000557 NADP binding site [chemical binding]; other site 358220000558 catalytic residues [active] 358220000559 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 358220000560 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 358220000561 putative active site [active] 358220000562 metal binding site [ion binding]; metal-binding site 358220000563 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220000564 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000565 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220000566 dimerization interface [polypeptide binding]; other site 358220000567 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 358220000568 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 358220000569 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 358220000570 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 358220000571 Ligand Binding Site [chemical binding]; other site 358220000572 putative protease; Provisional; Region: PRK15452 358220000573 Peptidase family U32; Region: Peptidase_U32; pfam01136 358220000574 Bacterial SH3 domain; Region: SH3_3; cl17532 358220000575 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 358220000576 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 358220000577 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220000578 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 358220000579 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220000580 acyl-activating enzyme (AAE) consensus motif; other site 358220000581 AMP binding site [chemical binding]; other site 358220000582 active site 358220000583 acyl-activating enzyme (AAE) consensus motif; other site 358220000584 CoA binding site [chemical binding]; other site 358220000585 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 358220000586 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 358220000587 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 358220000588 NAD(P) binding site [chemical binding]; other site 358220000589 Double zinc ribbon; Region: DZR; pfam12773 358220000590 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 358220000591 Double zinc ribbon; Region: DZR; pfam12773 358220000592 polyphosphate:nucleotide phosphotransferase, PPK2 family; Region: PPK2_rel_1; TIGR03709 358220000593 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 358220000594 conserved cys residue [active] 358220000595 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 358220000596 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220000597 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 358220000598 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 358220000599 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220000600 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000601 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220000602 dimerization interface [polypeptide binding]; other site 358220000603 Predicted membrane protein [Function unknown]; Region: COG4125 358220000604 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 358220000605 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 358220000606 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 358220000607 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 358220000608 substrate binding pocket [chemical binding]; other site 358220000609 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 358220000610 B12 binding site [chemical binding]; other site 358220000611 cobalt ligand [ion binding]; other site 358220000612 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 358220000613 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cl10015 358220000614 homotrimer interaction site [polypeptide binding]; other site 358220000615 putative active site [active] 358220000616 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220000617 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000618 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 358220000619 putative effector binding pocket; other site 358220000620 putative dimerization interface [polypeptide binding]; other site 358220000621 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220000622 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220000623 metal binding site [ion binding]; metal-binding site 358220000624 active site 358220000625 I-site; other site 358220000626 shikimate kinase; Reviewed; Region: aroK; PRK00131 358220000627 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 358220000628 ADP binding site [chemical binding]; other site 358220000629 magnesium binding site [ion binding]; other site 358220000630 putative shikimate binding site; other site 358220000631 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 358220000632 Beta-lactamase; Region: Beta-lactamase; pfam00144 358220000633 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08314 358220000634 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220000635 Putative long-chain fatty acid CoA ligase; Region: LC_FACS_like; cd05935 358220000636 acyl-activating enzyme (AAE) consensus motif; other site 358220000637 putative AMP binding site [chemical binding]; other site 358220000638 putative active site [active] 358220000639 putative CoA binding site [chemical binding]; other site 358220000640 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 358220000641 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220000642 NAD(P) binding site [chemical binding]; other site 358220000643 active site 358220000644 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 358220000645 Amidohydrolase; Region: Amidohydro_5; pfam13594 358220000646 Amidohydrolase; Region: Amidohydro_4; pfam13147 358220000647 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cd01292 358220000648 active site 358220000649 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220000650 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220000651 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 358220000652 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 358220000653 FAD binding pocket [chemical binding]; other site 358220000654 FAD binding motif [chemical binding]; other site 358220000655 phosphate binding motif [ion binding]; other site 358220000656 beta-alpha-beta structure motif; other site 358220000657 NAD binding pocket [chemical binding]; other site 358220000658 Ferredoxin [Energy production and conversion]; Region: COG1146 358220000659 4Fe-4S binding domain; Region: Fer4; pfam00037 358220000660 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 358220000661 hypothetical protein; Provisional; Region: PRK04334 358220000662 Amino acid synthesis; Region: AA_synth; pfam06684 358220000663 Amino acid synthesis; Region: AA_synth; pfam06684 358220000664 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_Arsenic_SBP_like; cd06330 358220000665 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220000666 putative ligand binding site [chemical binding]; other site 358220000667 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220000668 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220000669 TM-ABC transporter signature motif; other site 358220000670 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220000671 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220000672 TM-ABC transporter signature motif; other site 358220000673 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220000674 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220000675 Walker A/P-loop; other site 358220000676 ATP binding site [chemical binding]; other site 358220000677 Q-loop/lid; other site 358220000678 ABC transporter signature motif; other site 358220000679 Walker B; other site 358220000680 D-loop; other site 358220000681 H-loop/switch region; other site 358220000682 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220000683 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220000684 Walker A/P-loop; other site 358220000685 ATP binding site [chemical binding]; other site 358220000686 Q-loop/lid; other site 358220000687 ABC transporter signature motif; other site 358220000688 Walker B; other site 358220000689 D-loop; other site 358220000690 H-loop/switch region; other site 358220000691 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220000692 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220000693 putative ligand binding site [chemical binding]; other site 358220000694 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 358220000695 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 358220000696 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 358220000697 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220000698 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 358220000699 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 358220000700 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220000701 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 358220000702 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 358220000703 hypothetical protein; Provisional; Region: PRK02268 358220000704 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220000705 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220000706 putative DNA binding site [nucleotide binding]; other site 358220000707 putative Zn2+ binding site [ion binding]; other site 358220000708 AsnC family; Region: AsnC_trans_reg; pfam01037 358220000709 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 358220000710 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220000711 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 358220000712 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220000713 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 358220000714 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 358220000715 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220000716 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 358220000717 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 358220000718 AAA domain; Region: AAA_21; pfam13304 358220000719 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 358220000720 Walker B; other site 358220000721 D-loop; other site 358220000722 H-loop/switch region; other site 358220000723 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 358220000724 Uncharacterized conserved protein [Function unknown]; Region: COG2128 358220000725 Tannase and feruloyl esterase; Region: Tannase; pfam07519 358220000726 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220000727 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220000728 active site 358220000729 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220000730 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 358220000731 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 358220000732 NAD binding site [chemical binding]; other site 358220000733 homodimer interface [polypeptide binding]; other site 358220000734 homotetramer interface [polypeptide binding]; other site 358220000735 active site 358220000736 feruloyl-CoA synthase; Reviewed; Region: PRK08180 358220000737 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 358220000738 acyl-activating enzyme (AAE) consensus motif; other site 358220000739 putative AMP binding site [chemical binding]; other site 358220000740 putative active site [active] 358220000741 putative CoA binding site [chemical binding]; other site 358220000742 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 358220000743 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220000744 substrate binding site [chemical binding]; other site 358220000745 oxyanion hole (OAH) forming residues; other site 358220000746 trimer interface [polypeptide binding]; other site 358220000747 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cd01292 358220000748 active site 358220000749 Transcriptional regulators [Transcription]; Region: MarR; COG1846 358220000750 MarR family; Region: MarR_2; pfam12802 358220000751 MarR family; Region: MarR_2; cl17246 358220000752 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 358220000753 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 358220000754 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 358220000755 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 358220000756 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 358220000757 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 358220000758 Walker A/P-loop; other site 358220000759 ATP binding site [chemical binding]; other site 358220000760 Q-loop/lid; other site 358220000761 ABC transporter signature motif; other site 358220000762 Walker B; other site 358220000763 D-loop; other site 358220000764 H-loop/switch region; other site 358220000765 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 358220000766 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220000767 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220000768 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220000769 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220000770 DNA binding residues [nucleotide binding] 358220000771 dimerization interface [polypeptide binding]; other site 358220000772 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 358220000773 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 358220000774 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220000775 dimerization interface [polypeptide binding]; other site 358220000776 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220000777 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220000778 metal binding site [ion binding]; metal-binding site 358220000779 active site 358220000780 I-site; other site 358220000781 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220000782 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 358220000783 Outer membrane efflux protein; Region: OEP; pfam02321 358220000784 SnoaL-like domain; Region: SnoaL_3; pfam13474 358220000785 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 358220000786 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 358220000787 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 358220000788 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220000789 Walker A motif; other site 358220000790 ATP binding site [chemical binding]; other site 358220000791 Walker B motif; other site 358220000792 arginine finger; other site 358220000793 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 358220000794 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 358220000795 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 358220000796 Nitrogen regulatory protein P-II; Region: P-II; smart00938 358220000797 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 358220000798 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 358220000799 FAD binding domain; Region: FAD_binding_4; pfam01565 358220000800 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 358220000801 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 358220000802 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 358220000803 Cysteine-rich domain; Region: CCG; pfam02754 358220000804 Cysteine-rich domain; Region: CCG; pfam02754 358220000805 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 358220000806 DNA-binding site [nucleotide binding]; DNA binding site 358220000807 RNA-binding motif; other site 358220000808 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 358220000809 ProQ/FINO family; Region: ProQ; smart00945 358220000810 putative RNA binding sites [nucleotide binding]; other site 358220000811 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 358220000812 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220000813 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 358220000814 putative C-terminal domain interface [polypeptide binding]; other site 358220000815 putative GSH binding site (G-site) [chemical binding]; other site 358220000816 putative dimer interface [polypeptide binding]; other site 358220000817 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 358220000818 dimer interface [polypeptide binding]; other site 358220000819 N-terminal domain interface [polypeptide binding]; other site 358220000820 putative substrate binding pocket (H-site) [chemical binding]; other site 358220000821 Predicted transcriptional regulator [Transcription]; Region: COG2378 358220000822 HTH domain; Region: HTH_11; pfam08279 358220000823 WYL domain; Region: WYL; pfam13280 358220000824 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 358220000825 LytTr DNA-binding domain; Region: LytTR; smart00850 358220000826 glucans biosynthesis protein; Provisional; Region: opgC; PRK03854 358220000827 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 358220000828 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220000829 Coenzyme A binding pocket [chemical binding]; other site 358220000830 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 358220000831 catalytic residues [active] 358220000832 dimer interface [polypeptide binding]; other site 358220000833 EamA-like transporter family; Region: EamA; pfam00892 358220000834 lysophospholipid transporter LplT; Provisional; Region: PRK11195 358220000835 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220000836 alanine racemase; Reviewed; Region: dadX; PRK03646 358220000837 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 358220000838 active site 358220000839 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 358220000840 substrate binding site [chemical binding]; other site 358220000841 catalytic residues [active] 358220000842 dimer interface [polypeptide binding]; other site 358220000843 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 358220000844 MarR family; Region: MarR_2; pfam12802 358220000845 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 358220000846 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 358220000847 FAD binding pocket [chemical binding]; other site 358220000848 FAD binding motif [chemical binding]; other site 358220000849 phosphate binding motif [ion binding]; other site 358220000850 NAD binding pocket [chemical binding]; other site 358220000851 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 358220000852 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000853 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220000854 dimerization interface [polypeptide binding]; other site 358220000855 Lysine efflux permease [General function prediction only]; Region: COG1279 358220000856 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 358220000857 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 358220000858 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220000859 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 358220000860 C-terminal domain interface [polypeptide binding]; other site 358220000861 GSH binding site (G-site) [chemical binding]; other site 358220000862 dimer interface [polypeptide binding]; other site 358220000863 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 358220000864 N-terminal domain interface [polypeptide binding]; other site 358220000865 dimer interface [polypeptide binding]; other site 358220000866 substrate binding pocket (H-site) [chemical binding]; other site 358220000867 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 358220000868 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 358220000869 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 358220000870 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 358220000871 DNA repair protein RadA; Provisional; Region: PRK11823 358220000872 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 358220000873 Walker A motif/ATP binding site; other site 358220000874 ATP binding site [chemical binding]; other site 358220000875 Walker B motif; other site 358220000876 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 358220000877 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 358220000878 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 358220000879 homodimer interface [polypeptide binding]; other site 358220000880 substrate-cofactor binding pocket; other site 358220000881 catalytic residue [active] 358220000882 Zinc-finger domain; Region: zf-CHCC; cl01821 358220000883 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 358220000884 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 358220000885 putative metal binding site; other site 358220000886 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 358220000887 O-Antigen ligase; Region: Wzy_C; pfam04932 358220000888 This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant...; Region: GT1_AviGT4_like; cd03802 358220000889 putative ADP-binding pocket [chemical binding]; other site 358220000890 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220000891 Nitronate monooxygenase; Region: NMO; pfam03060 358220000892 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 358220000893 FMN binding site [chemical binding]; other site 358220000894 substrate binding site [chemical binding]; other site 358220000895 putative catalytic residue [active] 358220000896 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220000897 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220000898 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220000899 dimerization interface [polypeptide binding]; other site 358220000900 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 358220000901 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220000902 dimerization interface [polypeptide binding]; other site 358220000903 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220000904 dimer interface [polypeptide binding]; other site 358220000905 phosphorylation site [posttranslational modification] 358220000906 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220000907 ATP binding site [chemical binding]; other site 358220000908 Mg2+ binding site [ion binding]; other site 358220000909 G-X-G motif; other site 358220000910 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220000911 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220000912 active site 358220000913 phosphorylation site [posttranslational modification] 358220000914 intermolecular recognition site; other site 358220000915 dimerization interface [polypeptide binding]; other site 358220000916 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220000917 DNA binding site [nucleotide binding] 358220000918 AmpG-like permease; Region: 2A0125; TIGR00901 358220000919 Peptidase family M48; Region: Peptidase_M48; pfam01435 358220000920 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 358220000921 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220000922 PAS domain; Region: PAS_9; pfam13426 358220000923 putative active site [active] 358220000924 heme pocket [chemical binding]; other site 358220000925 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220000926 PAS domain; Region: PAS_9; pfam13426 358220000927 putative active site [active] 358220000928 heme pocket [chemical binding]; other site 358220000929 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220000930 PAS domain; Region: PAS_9; pfam13426 358220000931 putative active site [active] 358220000932 heme pocket [chemical binding]; other site 358220000933 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220000934 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220000935 dimer interface [polypeptide binding]; other site 358220000936 putative CheW interface [polypeptide binding]; other site 358220000937 Two component signalling adaptor domain; Region: CheW; smart00260 358220000938 GAF domain; Region: GAF; pfam01590 358220000939 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220000940 Response regulator receiver domain; Region: Response_reg; pfam00072 358220000941 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220000942 active site 358220000943 phosphorylation site [posttranslational modification] 358220000944 intermolecular recognition site; other site 358220000945 dimerization interface [polypeptide binding]; other site 358220000946 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 358220000947 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 358220000948 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220000949 Walker A motif; other site 358220000950 ATP binding site [chemical binding]; other site 358220000951 Walker B motif; other site 358220000952 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 358220000953 putative active site [active] 358220000954 putative catalytic site [active] 358220000955 putative DNA binding site [nucleotide binding]; other site 358220000956 putative phosphate binding site [ion binding]; other site 358220000957 metal binding site A [ion binding]; metal-binding site 358220000958 putative AP binding site [nucleotide binding]; other site 358220000959 putative metal binding site B [ion binding]; other site 358220000960 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220000961 active site 358220000962 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 358220000963 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 358220000964 GatB domain; Region: GatB_Yqey; smart00845 358220000965 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 358220000966 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 358220000967 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 358220000968 rod shape-determining protein MreB; Provisional; Region: PRK13927 358220000969 MreB and similar proteins; Region: MreB_like; cd10225 358220000970 nucleotide binding site [chemical binding]; other site 358220000971 Mg binding site [ion binding]; other site 358220000972 putative protofilament interaction site [polypeptide binding]; other site 358220000973 RodZ interaction site [polypeptide binding]; other site 358220000974 rod shape-determining protein MreC; Provisional; Region: PRK13922 358220000975 rod shape-determining protein MreC; Region: MreC; pfam04085 358220000976 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreD; COG2891 358220000977 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 358220000978 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 358220000979 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 358220000980 EamA-like transporter family; Region: EamA; pfam00892 358220000981 EamA-like transporter family; Region: EamA; pfam00892 358220000982 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 358220000983 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 358220000984 Walker A/P-loop; other site 358220000985 ATP binding site [chemical binding]; other site 358220000986 Q-loop/lid; other site 358220000987 ABC transporter signature motif; other site 358220000988 Walker B; other site 358220000989 D-loop; other site 358220000990 H-loop/switch region; other site 358220000991 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220000992 dimer interface [polypeptide binding]; other site 358220000993 conserved gate region; other site 358220000994 putative PBP binding loops; other site 358220000995 ABC-ATPase subunit interface; other site 358220000996 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220000997 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220000998 substrate binding pocket [chemical binding]; other site 358220000999 membrane-bound complex binding site; other site 358220001000 hinge residues; other site 358220001001 hypothetical protein; Provisional; Region: PRK10621 358220001002 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 358220001003 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 358220001004 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 358220001005 choline dehydrogenase; Validated; Region: PRK02106 358220001006 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 358220001007 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 358220001008 Permease; Region: Permease; pfam02405 358220001009 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 358220001010 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 358220001011 Walker A/P-loop; other site 358220001012 ATP binding site [chemical binding]; other site 358220001013 Q-loop/lid; other site 358220001014 ABC transporter signature motif; other site 358220001015 Walker B; other site 358220001016 D-loop; other site 358220001017 H-loop/switch region; other site 358220001018 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 358220001019 mce related protein; Region: MCE; pfam02470 358220001020 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 358220001021 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220001022 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4102 358220001023 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 358220001024 CsbD-like; Region: CsbD; cl17424 358220001025 Hemerythrin; Region: Hemerythrin; cd12107 358220001026 Fe binding site [ion binding]; other site 358220001027 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220001028 GAF domain; Region: GAF; pfam01590 358220001029 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220001030 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220001031 metal binding site [ion binding]; metal-binding site 358220001032 active site 358220001033 I-site; other site 358220001034 inner membrane protein; Provisional; Region: PRK11715 358220001035 sensory histidine kinase CreC; Provisional; Region: PRK11100 358220001036 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220001037 dimer interface [polypeptide binding]; other site 358220001038 phosphorylation site [posttranslational modification] 358220001039 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220001040 ATP binding site [chemical binding]; other site 358220001041 Mg2+ binding site [ion binding]; other site 358220001042 G-X-G motif; other site 358220001043 DNA-binding response regulator CreB; Provisional; Region: PRK11083 358220001044 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220001045 active site 358220001046 phosphorylation site [posttranslational modification] 358220001047 intermolecular recognition site; other site 358220001048 dimerization interface [polypeptide binding]; other site 358220001049 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220001050 DNA binding site [nucleotide binding] 358220001051 MarC family integral membrane protein; Region: MarC; cl00919 358220001052 short chain dehydrogenase; Provisional; Region: PRK06123 358220001053 classical (c) SDRs; Region: SDR_c; cd05233 358220001054 NAD(P) binding site [chemical binding]; other site 358220001055 active site 358220001056 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 358220001057 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 358220001058 active site 358220001059 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 358220001060 Thermotoga maritima CorA-like family; Region: TmCorA-like; cd12822 358220001061 oligomer interface [polypeptide binding]; other site 358220001062 metal binding site [ion binding]; metal-binding site 358220001063 metal binding site [ion binding]; metal-binding site 358220001064 putative Cl binding site [ion binding]; other site 358220001065 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 358220001066 aspartate ring; other site 358220001067 basic sphincter; other site 358220001068 hydrophobic gate; other site 358220001069 periplasmic entrance; other site 358220001070 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 358220001071 dimer interface [polypeptide binding]; other site 358220001072 active site 358220001073 aspartate-rich active site metal binding site; other site 358220001074 allosteric magnesium binding site [ion binding]; other site 358220001075 Schiff base residues; other site 358220001076 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 358220001077 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 358220001078 dimer interface [polypeptide binding]; other site 358220001079 [2Fe-2S] cluster binding site [ion binding]; other site 358220001080 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 358220001081 Serine hydrolase; Region: Ser_hydrolase; cl17834 358220001082 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 358220001083 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 358220001084 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 358220001085 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit...; Region: Ribosomal_S12; cd03368 358220001086 S17 interaction site [polypeptide binding]; other site 358220001087 S8 interaction site; other site 358220001088 16S rRNA interaction site [nucleotide binding]; other site 358220001089 streptomycin interaction site [chemical binding]; other site 358220001090 23S rRNA interaction site [nucleotide binding]; other site 358220001091 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 358220001092 30S ribosomal protein S7; Validated; Region: PRK05302 358220001093 elongation factor G; Reviewed; Region: PRK00007 358220001094 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 358220001095 G1 box; other site 358220001096 putative GEF interaction site [polypeptide binding]; other site 358220001097 GTP/Mg2+ binding site [chemical binding]; other site 358220001098 Switch I region; other site 358220001099 G2 box; other site 358220001100 G3 box; other site 358220001101 Switch II region; other site 358220001102 G4 box; other site 358220001103 G5 box; other site 358220001104 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 358220001105 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 358220001106 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 358220001107 elongation factor Tu; Reviewed; Region: PRK00049 358220001108 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 358220001109 G1 box; other site 358220001110 GEF interaction site [polypeptide binding]; other site 358220001111 GTP/Mg2+ binding site [chemical binding]; other site 358220001112 Switch I region; other site 358220001113 G2 box; other site 358220001114 G3 box; other site 358220001115 Switch II region; other site 358220001116 G4 box; other site 358220001117 G5 box; other site 358220001118 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 358220001119 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 358220001120 Antibiotic Binding Site [chemical binding]; other site 358220001121 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 358220001122 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 358220001123 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 358220001124 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 358220001125 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 358220001126 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 358220001127 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 358220001128 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 358220001129 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper...; Region: Ribosomal_L22; cd00336 358220001130 putative translocon binding site; other site 358220001131 protein-rRNA interface [nucleotide binding]; other site 358220001132 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 358220001133 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 358220001134 G-X-X-G motif; other site 358220001135 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 358220001136 Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with...; Region: Ribosomal_L16_L10e; cd01433 358220001137 23S rRNA interface [nucleotide binding]; other site 358220001138 5S rRNA interface [nucleotide binding]; other site 358220001139 putative antibiotic binding site [chemical binding]; other site 358220001140 L25 interface [polypeptide binding]; other site 358220001141 L27 interface [polypeptide binding]; other site 358220001142 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 358220001143 23S rRNA interface [nucleotide binding]; other site 358220001144 putative translocon interaction site; other site 358220001145 signal recognition particle (SRP54) interaction site; other site 358220001146 L23 interface [polypeptide binding]; other site 358220001147 trigger factor interaction site; other site 358220001148 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 358220001149 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 358220001150 catalytic triad [active] 358220001151 dimer interface [polypeptide binding]; other site 358220001152 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 358220001153 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220001154 Coenzyme A binding pocket [chemical binding]; other site 358220001155 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 358220001156 Cytochrome C' Region: Cytochrom_C_2; pfam01322 358220001157 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 358220001158 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 358220001159 catalytic residues [active] 358220001160 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220001161 putative substrate translocation pore; other site 358220001162 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220001163 active pocket/dimerization site; other site 358220001164 active site 358220001165 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cl00025 358220001166 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 358220001167 dimerization domain swap beta strand [polypeptide binding]; other site 358220001168 regulatory protein interface [polypeptide binding]; other site 358220001169 active site 358220001170 regulatory phosphorylation site [posttranslational modification]; other site 358220001171 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 358220001172 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 358220001173 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 358220001174 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 358220001175 aromatic amino acid exporter; Provisional; Region: PRK11689 358220001176 EamA-like transporter family; Region: EamA; cl17759 358220001177 Cupin domain; Region: Cupin_2; pfam07883 358220001178 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 358220001179 lipoyl synthase; Provisional; Region: PRK05481 358220001180 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220001181 FeS/SAM binding site; other site 358220001182 lipoate-protein ligase B; Provisional; Region: PRK14346 358220001183 Protein of unknown function (DUF493); Region: DUF493; cl01102 358220001184 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 358220001185 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 358220001186 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 358220001187 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 358220001188 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 358220001189 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 358220001190 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 358220001191 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 358220001192 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 358220001193 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 358220001194 beta subunit interaction interface [polypeptide binding]; other site 358220001195 Walker A motif; other site 358220001196 ATP binding site [chemical binding]; other site 358220001197 Walker B motif; other site 358220001198 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 358220001199 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 358220001200 core domain interface [polypeptide binding]; other site 358220001201 delta subunit interface [polypeptide binding]; other site 358220001202 epsilon subunit interface [polypeptide binding]; other site 358220001203 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 358220001204 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 358220001205 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 358220001206 alpha subunit interaction interface [polypeptide binding]; other site 358220001207 Walker A motif; other site 358220001208 ATP binding site [chemical binding]; other site 358220001209 Walker B motif; other site 358220001210 inhibitor binding site; inhibition site 358220001211 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 358220001212 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 358220001213 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 358220001214 gamma subunit interface [polypeptide binding]; other site 358220001215 epsilon subunit interface [polypeptide binding]; other site 358220001216 LBP interface [polypeptide binding]; other site 358220001217 Repair protein; Region: Repair_PSII; pfam04536 358220001218 Repair protein; Region: Repair_PSII; pfam04536 358220001219 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 358220001220 SnoaL-like domain; Region: SnoaL_3; pfam13474 358220001221 SnoaL-like domain; Region: SnoaL_2; pfam12680 358220001222 putative hydrolase; Provisional; Region: PRK10985 358220001223 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 358220001224 Cytochrome c; Region: Cytochrom_C; cl11414 358220001225 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 358220001226 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 358220001227 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 358220001228 HlyD family secretion protein; Region: HlyD; pfam00529 358220001229 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220001230 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 358220001231 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220001232 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 358220001233 elongation factor Tu; Reviewed; Region: PRK00049 358220001234 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 358220001235 G1 box; other site 358220001236 GEF interaction site [polypeptide binding]; other site 358220001237 GTP/Mg2+ binding site [chemical binding]; other site 358220001238 Switch I region; other site 358220001239 G2 box; other site 358220001240 G3 box; other site 358220001241 Switch II region; other site 358220001242 G4 box; other site 358220001243 G5 box; other site 358220001244 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 358220001245 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 358220001246 Antibiotic Binding Site [chemical binding]; other site 358220001247 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 358220001248 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 358220001249 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 358220001250 putative homodimer interface [polypeptide binding]; other site 358220001251 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 358220001252 heterodimer interface [polypeptide binding]; other site 358220001253 homodimer interface [polypeptide binding]; other site 358220001254 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 358220001255 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal...; Region: Ribosomal_L11; cd00349 358220001256 23S rRNA interface [nucleotide binding]; other site 358220001257 L7/L12 interface [polypeptide binding]; other site 358220001258 putative thiostrepton binding site; other site 358220001259 L25 interface [polypeptide binding]; other site 358220001260 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 358220001261 mRNA/rRNA interface [nucleotide binding]; other site 358220001262 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 358220001263 23S rRNA interface [nucleotide binding]; other site 358220001264 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 358220001265 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of...; Region: Ribosomal_L7_L12; cd00387 358220001266 peripheral dimer interface [polypeptide binding]; other site 358220001267 core dimer interface [polypeptide binding]; other site 358220001268 L10 interface [polypeptide binding]; other site 358220001269 L11 interface [polypeptide binding]; other site 358220001270 putative EF-Tu interaction site [polypeptide binding]; other site 358220001271 putative EF-G interaction site [polypeptide binding]; other site 358220001272 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 358220001273 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 358220001274 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 358220001275 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 358220001276 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 358220001277 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 358220001278 RPB3 interaction site [polypeptide binding]; other site 358220001279 RPB1 interaction site [polypeptide binding]; other site 358220001280 RPB11 interaction site [polypeptide binding]; other site 358220001281 RPB10 interaction site [polypeptide binding]; other site 358220001282 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 358220001283 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 358220001284 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 358220001285 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 358220001286 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 358220001287 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 358220001288 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 358220001289 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 358220001290 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 358220001291 DNA binding site [nucleotide binding] 358220001292 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 358220001293 LemA family; Region: LemA; cl00742 358220001294 16S rRNA methyltransferase B; Provisional; Region: PRK10901 358220001295 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 358220001296 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220001297 S-adenosylmethionine binding site [chemical binding]; other site 358220001298 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 358220001299 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220001300 dimerization interface [polypeptide binding]; other site 358220001301 PAS domain; Region: PAS; smart00091 358220001302 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 358220001303 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220001304 dimer interface [polypeptide binding]; other site 358220001305 phosphorylation site [posttranslational modification] 358220001306 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220001307 ATP binding site [chemical binding]; other site 358220001308 Mg2+ binding site [ion binding]; other site 358220001309 G-X-G motif; other site 358220001310 Response regulator receiver domain; Region: Response_reg; pfam00072 358220001311 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220001312 active site 358220001313 phosphorylation site [posttranslational modification] 358220001314 intermolecular recognition site; other site 358220001315 dimerization interface [polypeptide binding]; other site 358220001316 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 358220001317 sulfite reductase (NADPH) hemoprotein, beta-component; Region: CysI; TIGR02041 358220001318 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 358220001319 ThiF family; Region: ThiF; pfam00899 358220001320 ATP binding site [chemical binding]; other site 358220001321 Phage integrase family; Region: Phage_integrase; pfam00589 358220001322 active site 358220001323 DNA binding site [nucleotide binding] 358220001324 Int/Topo IB signature motif; other site 358220001325 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 358220001326 putative chaperone; Provisional; Region: PRK11678 358220001327 nucleotide binding site [chemical binding]; other site 358220001328 putative NEF/HSP70 interaction site [polypeptide binding]; other site 358220001329 SBD interface [polypeptide binding]; other site 358220001330 Predicted methyltransferases [General function prediction only]; Region: COG0313 358220001331 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 358220001332 putative SAM binding site [chemical binding]; other site 358220001333 putative homodimer interface [polypeptide binding]; other site 358220001334 hypothetical protein; Provisional; Region: PRK14673 358220001335 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 358220001336 dimer interface [polypeptide binding]; other site 358220001337 active site 358220001338 BON domain; Region: BON; pfam04972 358220001339 BON domain; Region: BON; pfam04972 358220001340 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 358220001341 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 358220001342 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 358220001343 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 358220001344 Walker A motif; other site 358220001345 ATP binding site [chemical binding]; other site 358220001346 Walker B motif; other site 358220001347 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220001348 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220001349 ligand binding site [chemical binding]; other site 358220001350 flexible hinge region; other site 358220001351 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 358220001352 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 358220001353 Walker A motif; other site 358220001354 ATP binding site [chemical binding]; other site 358220001355 Walker B motif; other site 358220001356 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 358220001357 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 358220001358 catalytic residue [active] 358220001359 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 358220001360 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 358220001361 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220001362 catalytic residue [active] 358220001363 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220001364 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 358220001365 putative ligand binding site [chemical binding]; other site 358220001366 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220001367 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220001368 acyl-CoA synthetase; Validated; Region: PRK06178 358220001369 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220001370 acyl-activating enzyme (AAE) consensus motif; other site 358220001371 AMP binding site [chemical binding]; other site 358220001372 active site 358220001373 CoA binding site [chemical binding]; other site 358220001374 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 358220001375 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 358220001376 ATP-grasp domain; Region: ATP-grasp_4; cl17255 358220001377 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 358220001378 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 358220001379 carboxyltransferase (CT) interaction site; other site 358220001380 biotinylation site [posttranslational modification]; other site 358220001381 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 358220001382 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 358220001383 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 358220001384 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 358220001385 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 358220001386 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 358220001387 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220001388 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220001389 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 358220001390 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220001391 catalytic residue [active] 358220001392 Predicted membrane protein [Function unknown]; Region: COG2733 358220001393 LrgB-like family; Region: LrgB; pfam04172 358220001394 LrgA family; Region: LrgA; pfam03788 358220001395 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 358220001396 FAD binding domain; Region: FAD_binding_4; pfam01565 358220001397 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220001398 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220001399 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 358220001400 dimerization interface [polypeptide binding]; other site 358220001401 substrate binding pocket [chemical binding]; other site 358220001402 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 358220001403 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 358220001404 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 358220001405 putative active site [active] 358220001406 putative substrate binding site [chemical binding]; other site 358220001407 putative cosubstrate binding site; other site 358220001408 catalytic site [active] 358220001409 PAS domain S-box; Region: sensory_box; TIGR00229 358220001410 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220001411 putative active site [active] 358220001412 heme pocket [chemical binding]; other site 358220001413 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220001414 PAS domain; Region: PAS_9; pfam13426 358220001415 putative active site [active] 358220001416 heme pocket [chemical binding]; other site 358220001417 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220001418 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220001419 metal binding site [ion binding]; metal-binding site 358220001420 active site 358220001421 I-site; other site 358220001422 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220001423 Protein of unknown function, DUF399; Region: DUF399; cl01139 358220001424 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 358220001425 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 358220001426 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220001427 dimerization interface [polypeptide binding]; other site 358220001428 GAF domain; Region: GAF; cl17456 358220001429 Histidine kinase; Region: HisKA_3; pfam07730 358220001430 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220001431 ATP binding site [chemical binding]; other site 358220001432 Mg2+ binding site [ion binding]; other site 358220001433 G-X-G motif; other site 358220001434 transcriptional regulator NarL; Provisional; Region: PRK10651 358220001435 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220001436 active site 358220001437 phosphorylation site [posttranslational modification] 358220001438 intermolecular recognition site; other site 358220001439 dimerization interface [polypeptide binding]; other site 358220001440 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220001441 DNA binding residues [nucleotide binding] 358220001442 dimerization interface [polypeptide binding]; other site 358220001443 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 358220001444 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220001445 putative substrate translocation pore; other site 358220001446 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 358220001447 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 358220001448 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 358220001449 [4Fe-4S] binding site [ion binding]; other site 358220001450 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 358220001451 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 358220001452 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 358220001453 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 358220001454 molybdopterin cofactor binding site; other site 358220001455 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 358220001456 4Fe-4S binding domain; Region: Fer4; cl02805 358220001457 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cl00470 358220001458 Nitrate reductase delta subunit [Energy production and conversion]; Region: NarJ; COG2180 358220001459 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 358220001460 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 358220001461 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 358220001462 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 358220001463 active site clefts [active] 358220001464 zinc binding site [ion binding]; other site 358220001465 dimer interface [polypeptide binding]; other site 358220001466 ribonucleotide reductase-like protein; Provisional; Region: PRK06948 358220001467 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 358220001468 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 358220001469 active site 358220001470 dimer interface [polypeptide binding]; other site 358220001471 effector binding site; other site 358220001472 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 358220001473 putative FMN binding site [chemical binding]; other site 358220001474 Hemerythrin-like domain; Region: Hr-like; cd12108 358220001475 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 358220001476 Putative ammonia monooxygenase; Region: AmoA; pfam05145 358220001477 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 358220001478 Protein of unknown function (DUF3567); Region: DUF3567; pfam12091 358220001479 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 358220001480 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 358220001481 Transcriptional regulator [Transcription]; Region: IclR; COG1414 358220001482 Bacterial transcriptional regulator; Region: IclR; pfam01614 358220001483 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 358220001484 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 358220001485 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220001486 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 358220001487 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220001488 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 358220001489 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 358220001490 putative NAD(P) binding site [chemical binding]; other site 358220001491 dimer interface [polypeptide binding]; other site 358220001492 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220001493 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220001494 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220001495 putative effector binding pocket; other site 358220001496 dimerization interface [polypeptide binding]; other site 358220001497 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 358220001498 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 358220001499 dimer interface [polypeptide binding]; other site 358220001500 active site 358220001501 metal binding site [ion binding]; metal-binding site 358220001502 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 358220001503 Predicted dienelactone hydrolase [General function prediction only]; Region: COG4188 358220001504 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 358220001505 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 358220001506 potential catalytic triad [active] 358220001507 conserved cys residue [active] 358220001508 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 358220001509 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 358220001510 putative [4Fe-4S] binding site [ion binding]; other site 358220001511 putative molybdopterin cofactor binding site [chemical binding]; other site 358220001512 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_3; cd02786 358220001513 putative molybdopterin cofactor binding site; other site 358220001514 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220001515 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220001516 putative ligand binding site [chemical binding]; other site 358220001517 acetylornithine deacetylase; Provisional; Region: PRK07522 358220001518 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 358220001519 metal binding site [ion binding]; metal-binding site 358220001520 putative dimer interface [polypeptide binding]; other site 358220001521 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 358220001522 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 358220001523 metal binding site [ion binding]; metal-binding site 358220001524 putative dimer interface [polypeptide binding]; other site 358220001525 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_6; cd06233 358220001526 putative active site [active] 358220001527 Zn binding site [ion binding]; other site 358220001528 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220001529 Integrase core domain; Region: rve; pfam00665 358220001530 Integrase core domain; Region: rve_3; cl15866 358220001531 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220001532 Helix-turn-helix domain; Region: HTH_38; pfam13936 358220001533 Bacterial protein of unknown function (DUF922); Region: DUF922; cl02415 358220001534 acyltransferase, WS/DGAT/MGAT; Region: acyl_WS_DGAT; TIGR02946 358220001535 Wax ester synthase-like Acyl-CoA acyltransferase domain; Region: WES_acyltransf; pfam03007 358220001536 Protein of unknown function (DUF1298); Region: DUF1298; pfam06974 358220001537 Acyl CoA binding protein; Region: ACBP; pfam00887 358220001538 acyl-CoA binding pocket [chemical binding]; other site 358220001539 CoA binding site [chemical binding]; other site 358220001540 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 358220001541 active site 358220001542 catalytic residues [active] 358220001543 metal binding site [ion binding]; metal-binding site 358220001544 ornithine cyclodeaminase; Validated; Region: PRK07589 358220001545 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 358220001546 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 358220001547 putative FMN binding site [chemical binding]; other site 358220001548 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; pfam09650 358220001549 Predicted aminopeptidase (DUF2265); Region: DUF2265; cl17720 358220001550 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 358220001551 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220001552 putative substrate translocation pore; other site 358220001553 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 358220001554 ArsC family; Region: ArsC; pfam03960 358220001555 catalytic residues [active] 358220001556 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 358220001557 AAA domain; Region: AAA_33; pfam13671 358220001558 putative phosphonate metabolism protein; Region: Phn_opern_protn; TIGR03223 358220001559 phosphonates metabolism transcriptional regulator PhnF; Region: C_P_lyase_phnF; TIGR02325 358220001560 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220001561 DNA-binding site [nucleotide binding]; DNA binding site 358220001562 UTRA domain; Region: UTRA; pfam07702 358220001563 Phosphonate metabolism protein PhnG; Region: PhnG; pfam06754 358220001564 Bacterial phosphonate metabolism protein (PhnH); Region: PhnH; pfam05845 358220001565 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; pfam05861 358220001566 Phosphonate metabolism protein PhnJ; Region: PhnJ; pfam06007 358220001567 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 358220001568 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220001569 Coenzyme A binding pocket [chemical binding]; other site 358220001570 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 358220001571 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 358220001572 Walker A/P-loop; other site 358220001573 ATP binding site [chemical binding]; other site 358220001574 Q-loop/lid; other site 358220001575 ABC transporter signature motif; other site 358220001576 Walker B; other site 358220001577 D-loop; other site 358220001578 H-loop/switch region; other site 358220001579 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 358220001580 phosphonate C-P lyase system protein PhnL; Region: CP_lyasePhnL; TIGR02324 358220001581 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220001582 Walker A/P-loop; other site 358220001583 ATP binding site [chemical binding]; other site 358220001584 Q-loop/lid; other site 358220001585 ABC transporter signature motif; other site 358220001586 Walker B; other site 358220001587 D-loop; other site 358220001588 H-loop/switch region; other site 358220001589 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 358220001590 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 358220001591 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 358220001592 active site 358220001593 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 358220001594 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 358220001595 Walker A/P-loop; other site 358220001596 ATP binding site [chemical binding]; other site 358220001597 Q-loop/lid; other site 358220001598 ABC transporter signature motif; other site 358220001599 Walker B; other site 358220001600 D-loop; other site 358220001601 H-loop/switch region; other site 358220001602 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 358220001603 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 358220001604 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220001605 dimer interface [polypeptide binding]; other site 358220001606 conserved gate region; other site 358220001607 ABC-ATPase subunit interface; other site 358220001608 phosphonate degradation operons associated HDIG domain protein; Region: Phn-HD; TIGR03276 358220001609 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 358220001610 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 358220001611 conserved cys residue [active] 358220001612 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 358220001613 DJ-1 family protein; Region: not_thiJ; TIGR01383 358220001614 conserved cys residue [active] 358220001615 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220001616 putative DNA binding site [nucleotide binding]; other site 358220001617 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 358220001618 putative Zn2+ binding site [ion binding]; other site 358220001619 AsnC family; Region: AsnC_trans_reg; pfam01037 358220001620 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 358220001621 EamA-like transporter family; Region: EamA; pfam00892 358220001622 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 358220001623 homotrimer interaction site [polypeptide binding]; other site 358220001624 putative active site [active] 358220001625 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220001626 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 358220001627 acyl-activating enzyme (AAE) consensus motif; other site 358220001628 AMP binding site [chemical binding]; other site 358220001629 active site 358220001630 CoA binding site [chemical binding]; other site 358220001631 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220001632 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 358220001633 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 358220001634 active site 358220001635 enoyl-CoA hydratase; Provisional; Region: PRK06688 358220001636 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220001637 substrate binding site [chemical binding]; other site 358220001638 oxyanion hole (OAH) forming residues; other site 358220001639 trimer interface [polypeptide binding]; other site 358220001640 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 358220001641 MarR family; Region: MarR; pfam01047 358220001642 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 358220001643 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 358220001644 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220001645 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 358220001646 active site 358220001647 FMN binding site [chemical binding]; other site 358220001648 substrate binding site [chemical binding]; other site 358220001649 homotetramer interface [polypeptide binding]; other site 358220001650 catalytic residue [active] 358220001651 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 358220001652 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220001653 S-adenosylmethionine binding site [chemical binding]; other site 358220001654 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 358220001655 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220001656 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220001657 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 358220001658 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220001659 acyl-activating enzyme (AAE) consensus motif; other site 358220001660 active site 358220001661 AMP binding site [chemical binding]; other site 358220001662 CoA binding site [chemical binding]; other site 358220001663 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220001664 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220001665 Walker A/P-loop; other site 358220001666 ATP binding site [chemical binding]; other site 358220001667 Q-loop/lid; other site 358220001668 ABC transporter signature motif; other site 358220001669 Walker B; other site 358220001670 D-loop; other site 358220001671 H-loop/switch region; other site 358220001672 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 358220001673 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220001674 putative ligand binding site [chemical binding]; other site 358220001675 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220001676 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220001677 TM-ABC transporter signature motif; other site 358220001678 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220001679 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220001680 TM-ABC transporter signature motif; other site 358220001681 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220001682 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220001683 Walker A/P-loop; other site 358220001684 ATP binding site [chemical binding]; other site 358220001685 Q-loop/lid; other site 358220001686 ABC transporter signature motif; other site 358220001687 Walker B; other site 358220001688 D-loop; other site 358220001689 H-loop/switch region; other site 358220001690 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 358220001691 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220001692 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 358220001693 acyl-activating enzyme (AAE) consensus motif; other site 358220001694 putative AMP binding site [chemical binding]; other site 358220001695 putative active site [active] 358220001696 putative CoA binding site [chemical binding]; other site 358220001697 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 358220001698 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220001699 Walker A motif; other site 358220001700 ATP binding site [chemical binding]; other site 358220001701 Walker B motif; other site 358220001702 arginine finger; other site 358220001703 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220001704 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220001705 putative ligand binding site [chemical binding]; other site 358220001706 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220001707 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220001708 ligand binding site [chemical binding]; other site 358220001709 flexible hinge region; other site 358220001710 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 358220001711 non-specific DNA interactions [nucleotide binding]; other site 358220001712 DNA binding site [nucleotide binding] 358220001713 sequence specific DNA binding site [nucleotide binding]; other site 358220001714 putative cAMP binding site [chemical binding]; other site 358220001715 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220001716 dimerization interface [polypeptide binding]; other site 358220001717 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220001718 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220001719 dimer interface [polypeptide binding]; other site 358220001720 putative CheW interface [polypeptide binding]; other site 358220001721 Domain of unknown function (DUF4394); Region: DUF4394; pfam14339 358220001722 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220001723 dimerization interface [polypeptide binding]; other site 358220001724 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220001725 metal binding site [ion binding]; metal-binding site 358220001726 active site 358220001727 I-site; other site 358220001728 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220001729 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 358220001730 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 358220001731 RNA binding surface [nucleotide binding]; other site 358220001732 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 358220001733 active site 358220001734 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 358220001735 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 358220001736 heat shock protein 90; Provisional; Region: PRK05218 358220001737 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220001738 ATP binding site [chemical binding]; other site 358220001739 Mg2+ binding site [ion binding]; other site 358220001740 G-X-G motif; other site 358220001741 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220001742 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220001743 active site 358220001744 phosphorylation site [posttranslational modification] 358220001745 intermolecular recognition site; other site 358220001746 dimerization interface [polypeptide binding]; other site 358220001747 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220001748 DNA binding site [nucleotide binding] 358220001749 serine/threonine protein kinase; Provisional; Region: PRK11768 358220001750 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 358220001751 Protein of unknown function (DUF2855); Region: DUF2855; pfam11017 358220001752 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 358220001753 Catalytic domain of Protein Kinases; Region: PKc; cd00180 358220001754 active site 358220001755 ATP binding site [chemical binding]; other site 358220001756 substrate binding site [chemical binding]; other site 358220001757 activation loop (A-loop); other site 358220001758 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 358220001759 Ligand Binding Site [chemical binding]; other site 358220001760 Calcineurin-like phosphoesterase superfamily domain; Region: Metallophos_2; pfam12850 358220001761 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 358220001762 active site 358220001763 metal binding site [ion binding]; metal-binding site 358220001764 Protein of unknown function (DUF1304); Region: DUF1304; pfam06993 358220001765 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 358220001766 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 358220001767 MarR family; Region: MarR; pfam01047 358220001768 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220001769 enoyl-CoA hydratase; Provisional; Region: PRK06563 358220001770 substrate binding site [chemical binding]; other site 358220001771 oxyanion hole (OAH) forming residues; other site 358220001772 trimer interface [polypeptide binding]; other site 358220001773 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 358220001774 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220001775 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220001776 choline dehydrogenase; Validated; Region: PRK02106 358220001777 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 358220001778 Hemerythrin-like domain of FBXL5-like proteins; Region: Hr_FBXL5; cd12109 358220001779 Fe binding site [ion binding]; other site 358220001780 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 358220001781 GAF domain; Region: GAF; pfam01590 358220001782 ABC-2 type transporter; Region: ABC2_membrane; cl17235 358220001783 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 358220001784 PAS domain S-box; Region: sensory_box; TIGR00229 358220001785 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220001786 putative active site [active] 358220001787 heme pocket [chemical binding]; other site 358220001788 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 358220001789 Histidine kinase; Region: HisKA_3; pfam07730 358220001790 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220001791 ATP binding site [chemical binding]; other site 358220001792 Mg2+ binding site [ion binding]; other site 358220001793 G-X-G motif; other site 358220001794 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220001795 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220001796 active site 358220001797 phosphorylation site [posttranslational modification] 358220001798 intermolecular recognition site; other site 358220001799 dimerization interface [polypeptide binding]; other site 358220001800 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220001801 DNA binding residues [nucleotide binding] 358220001802 dimerization interface [polypeptide binding]; other site 358220001803 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 358220001804 NMT1-like family; Region: NMT1_2; pfam13379 358220001805 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 358220001806 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220001807 dimer interface [polypeptide binding]; other site 358220001808 conserved gate region; other site 358220001809 putative PBP binding loops; other site 358220001810 ABC-ATPase subunit interface; other site 358220001811 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 358220001812 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 358220001813 Walker A/P-loop; other site 358220001814 ATP binding site [chemical binding]; other site 358220001815 Q-loop/lid; other site 358220001816 ABC transporter signature motif; other site 358220001817 Walker B; other site 358220001818 D-loop; other site 358220001819 H-loop/switch region; other site 358220001820 cyanate hydratase; Validated; Region: PRK02866 358220001821 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 358220001822 oligomer interface [polypeptide binding]; other site 358220001823 active site 358220001824 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5343 358220001825 Anti-sigma-K factor rskA; Region: RskA; pfam10099 358220001826 RNA polymerase sigma factor; Provisional; Region: PRK12537 358220001827 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220001828 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220001829 DNA binding residues [nucleotide binding] 358220001830 Protein of unknown function (DUF3455); Region: DUF3455; pfam11937 358220001831 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 358220001832 Rubredoxin; Region: Rubredoxin; pfam00301 358220001833 iron binding site [ion binding]; other site 358220001834 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 358220001835 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220001836 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220001837 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220001838 active site 358220001839 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220001840 OsmC-like protein; Region: OsmC; pfam02566 358220001841 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 358220001842 Rhodanese-like domain; Region: Rhodanese; pfam00581 358220001843 active site residue [active] 358220001844 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 358220001845 active site residue [active] 358220001846 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220001847 GAF domain; Region: GAF; pfam01590 358220001848 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 358220001849 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220001850 Walker A motif; other site 358220001851 ATP binding site [chemical binding]; other site 358220001852 Walker B motif; other site 358220001853 arginine finger; other site 358220001854 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 358220001855 Cytochrome c; Region: Cytochrom_C; pfam00034 358220001856 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 358220001857 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 358220001858 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 358220001859 active site 358220001860 Fe binding site [ion binding]; other site 358220001861 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220001862 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220001863 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 358220001864 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 358220001865 ATP-grasp domain; Region: ATP-grasp; pfam02222 358220001866 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 358220001867 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220001868 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220001869 metal binding site [ion binding]; metal-binding site 358220001870 active site 358220001871 I-site; other site 358220001872 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220001873 nodulation ABC transporter NodI; Provisional; Region: PRK13537 358220001874 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 358220001875 Walker A/P-loop; other site 358220001876 ATP binding site [chemical binding]; other site 358220001877 Q-loop/lid; other site 358220001878 ABC transporter signature motif; other site 358220001879 Walker B; other site 358220001880 D-loop; other site 358220001881 H-loop/switch region; other site 358220001882 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 358220001883 cofactor binding site; other site 358220001884 metal binding site [ion binding]; metal-binding site 358220001885 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 358220001886 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 358220001887 dimer interface [polypeptide binding]; other site 358220001888 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 358220001889 active site 358220001890 Fe binding site [ion binding]; other site 358220001891 lipase chaperone; Provisional; Region: PRK01294 358220001892 Proteobacterial lipase chaperone protein; Region: Lipase_chap; pfam03280 358220001893 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 358220001894 Lipase (class 2); Region: Lipase_2; pfam01674 358220001895 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220001896 dimerization interface [polypeptide binding]; other site 358220001897 putative DNA binding site [nucleotide binding]; other site 358220001898 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220001899 putative Zn2+ binding site [ion binding]; other site 358220001900 AsnC family; Region: AsnC_trans_reg; pfam01037 358220001901 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 358220001902 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220001903 Coenzyme A binding pocket [chemical binding]; other site 358220001904 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 358220001905 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 358220001906 Transporter associated domain; Region: CorC_HlyC; smart01091 358220001907 apolipoprotein N-acyltransferase; Region: lnt; TIGR00546 358220001908 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 358220001909 putative active site [active] 358220001910 catalytic triad [active] 358220001911 putative dimer interface [polypeptide binding]; other site 358220001912 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 358220001913 dimer interface [polypeptide binding]; other site 358220001914 active site 1 [active] 358220001915 active site 2 [active] 358220001916 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 358220001917 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 358220001918 dimer interface [polypeptide binding]; other site 358220001919 active site 358220001920 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220001921 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220001922 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220001923 dimerization interface [polypeptide binding]; other site 358220001924 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 358220001925 homodimer interface [polypeptide binding]; other site 358220001926 active site 358220001927 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 358220001928 dimer interface [polypeptide binding]; other site 358220001929 motif 1; other site 358220001930 active site 358220001931 motif 2; other site 358220001932 motif 3; other site 358220001933 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 358220001934 DALR anticodon binding domain; Region: DALR_1; pfam05746 358220001935 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 358220001936 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220001937 active site 358220001938 motif I; other site 358220001939 motif II; other site 358220001940 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 358220001941 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 358220001942 putative acyl-acceptor binding pocket; other site 358220001943 Protein of unknown function DUF45; Region: DUF45; pfam01863 358220001944 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 358220001945 active site residue [active] 358220001946 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 358220001947 BON domain; Region: BON; pfam04972 358220001948 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 358220001949 pantothenate kinase; Reviewed; Region: PRK13329 358220001950 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 358220001951 TPR motif; other site 358220001952 binding surface 358220001953 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220001954 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220001955 Bacterial transcriptional repressor; Region: TetR; pfam13972 358220001956 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; pfam05597 358220001957 short chain dehydrogenase; Provisional; Region: PRK07201 358220001958 Pseudomonas fluorescens MupV-like, extended (e) SDRs; Region: MupV_like_SDR_e; cd05263 358220001959 putative NAD(P) binding site [chemical binding]; other site 358220001960 active site 358220001961 putative substrate binding site [chemical binding]; other site 358220001962 classical (c) SDRs; Region: SDR_c; cd05233 358220001963 NAD(P) binding site [chemical binding]; other site 358220001964 active site 358220001965 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 358220001966 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 358220001967 NAD binding site [chemical binding]; other site 358220001968 substrate binding site [chemical binding]; other site 358220001969 homodimer interface [polypeptide binding]; other site 358220001970 active site 358220001971 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 358220001972 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 358220001973 NADP binding site [chemical binding]; other site 358220001974 active site 358220001975 putative substrate binding site [chemical binding]; other site 358220001976 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 358220001977 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 358220001978 substrate binding site; other site 358220001979 tetramer interface; other site 358220001980 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 358220001981 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 358220001982 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 358220001983 Substrate binding site; other site 358220001984 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 358220001985 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 358220001986 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 358220001987 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 358220001988 Walker A/P-loop; other site 358220001989 ATP binding site [chemical binding]; other site 358220001990 Q-loop/lid; other site 358220001991 ABC transporter signature motif; other site 358220001992 Walker B; other site 358220001993 D-loop; other site 358220001994 H-loop/switch region; other site 358220001995 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 358220001996 putative carbohydrate binding site [chemical binding]; other site 358220001997 Methyltransferase domain; Region: Methyltransf_23; pfam13489 358220001998 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220001999 S-adenosylmethionine binding site [chemical binding]; other site 358220002000 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 358220002001 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220002002 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 358220002003 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220002004 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 358220002005 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220002006 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 358220002007 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 358220002008 Ligand binding site; other site 358220002009 Putative Catalytic site; other site 358220002010 DXD motif; other site 358220002011 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 358220002012 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 358220002013 NADP-binding site; other site 358220002014 homotetramer interface [polypeptide binding]; other site 358220002015 substrate binding site [chemical binding]; other site 358220002016 homodimer interface [polypeptide binding]; other site 358220002017 active site 358220002018 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 358220002019 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220002020 NAD(P) binding site [chemical binding]; other site 358220002021 active site 358220002022 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220002023 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 358220002024 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220002025 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 358220002026 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 358220002027 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 358220002028 Probable Catalytic site; other site 358220002029 metal-binding site 358220002030 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 358220002031 SapC; Region: SapC; pfam07277 358220002032 ATP-grasp domain; Region: ATP-grasp_4; cl17255 358220002033 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 358220002034 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220002035 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 358220002036 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 358220002037 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220002038 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 358220002039 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220002040 Walker A/P-loop; other site 358220002041 ATP binding site [chemical binding]; other site 358220002042 Q-loop/lid; other site 358220002043 ABC transporter signature motif; other site 358220002044 Walker B; other site 358220002045 D-loop; other site 358220002046 H-loop/switch region; other site 358220002047 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 358220002048 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 358220002049 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 358220002050 Walker A/P-loop; other site 358220002051 ATP binding site [chemical binding]; other site 358220002052 Q-loop/lid; other site 358220002053 ABC transporter signature motif; other site 358220002054 Walker B; other site 358220002055 D-loop; other site 358220002056 H-loop/switch region; other site 358220002057 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 358220002058 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220002059 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220002060 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 358220002061 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which...; Region: GT_MraY_like; cd06912 358220002062 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 358220002063 Mg++ binding site [ion binding]; other site 358220002064 putative catalytic motif [active] 358220002065 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 358220002066 feedback inhibition sensing region; other site 358220002067 homohexameric interface [polypeptide binding]; other site 358220002068 nucleotide binding site [chemical binding]; other site 358220002069 N-acetyl-L-glutamate binding site [chemical binding]; other site 358220002070 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220002071 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220002072 active site 358220002073 phosphorylation site [posttranslational modification] 358220002074 intermolecular recognition site; other site 358220002075 dimerization interface [polypeptide binding]; other site 358220002076 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220002077 DNA binding site [nucleotide binding] 358220002078 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 358220002079 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220002080 dimer interface [polypeptide binding]; other site 358220002081 phosphorylation site [posttranslational modification] 358220002082 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220002083 ATP binding site [chemical binding]; other site 358220002084 Mg2+ binding site [ion binding]; other site 358220002085 G-X-G motif; other site 358220002086 division inhibitor protein; Provisional; Region: slmA; PRK09480 358220002087 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220002088 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220002089 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220002090 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 358220002091 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 358220002092 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220002093 active site 358220002094 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 358220002095 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 358220002096 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 358220002097 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220002098 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220002099 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220002100 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220002101 substrate binding site [chemical binding]; other site 358220002102 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 358220002103 oxyanion hole (OAH) forming residues; other site 358220002104 trimer interface [polypeptide binding]; other site 358220002105 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220002106 CoenzymeA binding site [chemical binding]; other site 358220002107 subunit interaction site [polypeptide binding]; other site 358220002108 PHB binding site; other site 358220002109 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 358220002110 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220002111 dimer interface [polypeptide binding]; other site 358220002112 active site 358220002113 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 358220002114 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 358220002115 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 358220002116 enoyl-CoA hydratase; Provisional; Region: PRK06688 358220002117 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220002118 substrate binding site [chemical binding]; other site 358220002119 oxyanion hole (OAH) forming residues; other site 358220002120 trimer interface [polypeptide binding]; other site 358220002121 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220002122 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220002123 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 358220002124 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 358220002125 NAD(P) binding site [chemical binding]; other site 358220002126 substrate binding site [chemical binding]; other site 358220002127 homotetramer interface [polypeptide binding]; other site 358220002128 active site 358220002129 homodimer interface [polypeptide binding]; other site 358220002130 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 358220002131 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 358220002132 DNA alkylation repair enzyme [DNA replication, recombination, and repair]; Region: COG4335 358220002133 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220002134 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220002135 active site 358220002136 enoyl-CoA hydratase; Provisional; Region: PRK05995 358220002137 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220002138 substrate binding site [chemical binding]; other site 358220002139 oxyanion hole (OAH) forming residues; other site 358220002140 trimer interface [polypeptide binding]; other site 358220002141 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 358220002142 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 358220002143 ATP-grasp domain; Region: ATP-grasp_4; cl17255 358220002144 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 358220002145 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 358220002146 carboxyltransferase (CT) interaction site; other site 358220002147 biotinylation site [posttranslational modification]; other site 358220002148 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220002149 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220002150 active site 358220002151 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 358220002152 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 358220002153 putative active site [active] 358220002154 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 358220002155 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220002156 substrate binding site [chemical binding]; other site 358220002157 oxyanion hole (OAH) forming residues; other site 358220002158 trimer interface [polypeptide binding]; other site 358220002159 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220002160 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220002161 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 358220002162 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220002163 dimer interface [polypeptide binding]; other site 358220002164 active site 358220002165 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220002166 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220002167 active site 358220002168 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 358220002169 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220002170 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 358220002171 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220002172 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220002173 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 358220002174 acyl-activating enzyme (AAE) consensus motif; other site 358220002175 acyl-activating enzyme (AAE) consensus motif; other site 358220002176 putative AMP binding site [chemical binding]; other site 358220002177 putative active site [active] 358220002178 putative CoA binding site [chemical binding]; other site 358220002179 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220002180 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220002181 Walker A/P-loop; other site 358220002182 ATP binding site [chemical binding]; other site 358220002183 Q-loop/lid; other site 358220002184 ABC transporter signature motif; other site 358220002185 Walker B; other site 358220002186 D-loop; other site 358220002187 H-loop/switch region; other site 358220002188 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220002189 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220002190 Walker A/P-loop; other site 358220002191 ATP binding site [chemical binding]; other site 358220002192 Q-loop/lid; other site 358220002193 ABC transporter signature motif; other site 358220002194 Walker B; other site 358220002195 D-loop; other site 358220002196 H-loop/switch region; other site 358220002197 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220002198 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220002199 TM-ABC transporter signature motif; other site 358220002200 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220002201 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220002202 TM-ABC transporter signature motif; other site 358220002203 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 358220002204 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220002205 substrate binding site [chemical binding]; other site 358220002206 oxyanion hole (OAH) forming residues; other site 358220002207 trimer interface [polypeptide binding]; other site 358220002208 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220002209 CoenzymeA binding site [chemical binding]; other site 358220002210 subunit interaction site [polypeptide binding]; other site 358220002211 PHB binding site; other site 358220002212 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 358220002213 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 358220002214 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 358220002215 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 358220002216 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220002217 Walker A/P-loop; other site 358220002218 ATP binding site [chemical binding]; other site 358220002219 Q-loop/lid; other site 358220002220 ABC transporter signature motif; other site 358220002221 Walker B; other site 358220002222 D-loop; other site 358220002223 H-loop/switch region; other site 358220002224 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 358220002225 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 358220002226 putative ligand binding site [chemical binding]; other site 358220002227 NAD binding site [chemical binding]; other site 358220002228 catalytic site [active] 358220002229 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 358220002230 homodimer interface [polypeptide binding]; other site 358220002231 chemical substrate binding site [chemical binding]; other site 358220002232 oligomer interface [polypeptide binding]; other site 358220002233 metal binding site [ion binding]; metal-binding site 358220002234 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220002235 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 358220002236 DctM-like transporters; Region: DctM; pfam06808 358220002237 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 358220002238 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 358220002239 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220002240 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220002241 dimerization interface [polypeptide binding]; other site 358220002242 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 358220002243 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220002244 substrate binding pocket [chemical binding]; other site 358220002245 membrane-bound complex binding site; other site 358220002246 hinge residues; other site 358220002247 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 358220002248 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220002249 substrate binding pocket [chemical binding]; other site 358220002250 membrane-bound complex binding site; other site 358220002251 hinge residues; other site 358220002252 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220002253 dimer interface [polypeptide binding]; other site 358220002254 conserved gate region; other site 358220002255 putative PBP binding loops; other site 358220002256 ABC-ATPase subunit interface; other site 358220002257 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220002258 dimer interface [polypeptide binding]; other site 358220002259 conserved gate region; other site 358220002260 putative PBP binding loops; other site 358220002261 ABC-ATPase subunit interface; other site 358220002262 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 358220002263 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 358220002264 Walker A/P-loop; other site 358220002265 ATP binding site [chemical binding]; other site 358220002266 Q-loop/lid; other site 358220002267 ABC transporter signature motif; other site 358220002268 Walker B; other site 358220002269 D-loop; other site 358220002270 H-loop/switch region; other site 358220002271 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 358220002272 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 358220002273 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 358220002274 putative active site [active] 358220002275 glutamate carboxypeptidase; Reviewed; Region: PRK06133 358220002276 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 358220002277 metal binding site [ion binding]; metal-binding site 358220002278 dimer interface [polypeptide binding]; other site 358220002279 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220002280 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 358220002281 active site 358220002282 substrate binding pocket [chemical binding]; other site 358220002283 dimer interface [polypeptide binding]; other site 358220002284 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 358220002285 heat shock protein HtpX; Provisional; Region: PRK05457 358220002286 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220002287 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 358220002288 dimerization interface [polypeptide binding]; other site 358220002289 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220002290 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220002291 dimer interface [polypeptide binding]; other site 358220002292 putative CheW interface [polypeptide binding]; other site 358220002293 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 358220002294 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 358220002295 transmembrane helices; other site 358220002296 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 358220002297 conserved cys residue [active] 358220002298 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 358220002299 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220002300 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like2; cd05667 358220002301 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 358220002302 metal binding site [ion binding]; metal-binding site 358220002303 putative dimer interface [polypeptide binding]; other site 358220002304 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 358220002305 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 358220002306 Predicted integral membrane protein [Function unknown]; Region: COG0392 358220002307 cardiolipin synthase 2; Provisional; Region: PRK11263 358220002308 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 358220002309 putative active site [active] 358220002310 catalytic site [active] 358220002311 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 358220002312 putative active site [active] 358220002313 catalytic site [active] 358220002314 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 358220002315 putative catalytic site [active] 358220002316 putative metal binding site [ion binding]; other site 358220002317 putative phosphate binding site [ion binding]; other site 358220002318 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 358220002319 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 358220002320 dimer interface [polypeptide binding]; other site 358220002321 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220002322 catalytic residue [active] 358220002323 RNA 3'-terminal-phosphate cyclase; Provisional; Region: PRK04204 358220002324 This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats...; Region: EPT_RTPC-like; cl00288 358220002325 putative active site [active] 358220002326 Predicted nucleotidyltransferase; Region: Nuc-transf; pfam10127 358220002327 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 358220002328 hypothetical protein; Reviewed; Region: PRK09588 358220002329 Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: RtcR; COG4650 358220002330 Regulator of RNA terminal phosphate cyclase; Region: RtcR; pfam06956 358220002331 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220002332 Walker A motif; other site 358220002333 ATP binding site [chemical binding]; other site 358220002334 Walker B motif; other site 358220002335 arginine finger; other site 358220002336 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 358220002337 Bacterial protein of unknown function (DUF898); Region: DUF898; pfam05987 358220002338 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 358220002339 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 358220002340 RNA binding surface [nucleotide binding]; other site 358220002341 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 358220002342 active site 358220002343 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 358220002344 nudix motif; other site 358220002345 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 358220002346 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 358220002347 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220002348 putative substrate translocation pore; other site 358220002349 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220002350 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220002351 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220002352 dimerization interface [polypeptide binding]; other site 358220002353 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220002354 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 358220002355 C-terminal domain interface [polypeptide binding]; other site 358220002356 GSH binding site (G-site) [chemical binding]; other site 358220002357 dimer interface [polypeptide binding]; other site 358220002358 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 358220002359 dimer interface [polypeptide binding]; other site 358220002360 N-terminal domain interface [polypeptide binding]; other site 358220002361 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 358220002362 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 358220002363 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 358220002364 Protein of unknown function, DUF484; Region: DUF484; cl17449 358220002365 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 358220002366 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220002367 active site 358220002368 DNA binding site [nucleotide binding] 358220002369 Int/Topo IB signature motif; other site 358220002370 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 358220002371 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 358220002372 Catalytic site [active] 358220002373 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 358220002374 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220002375 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220002376 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220002377 dimer interface [polypeptide binding]; other site 358220002378 putative CheW interface [polypeptide binding]; other site 358220002379 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 358220002380 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 358220002381 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 358220002382 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 358220002383 putative RNA binding site [nucleotide binding]; other site 358220002384 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220002385 S-adenosylmethionine binding site [chemical binding]; other site 358220002386 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 358220002387 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 358220002388 P-loop, Walker A motif; other site 358220002389 Base recognition motif; other site 358220002390 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 358220002391 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 358220002392 STAS domain; Region: STAS_2; pfam13466 358220002393 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 358220002394 active site 358220002395 HslU subunit interaction site [polypeptide binding]; other site 358220002396 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 358220002397 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220002398 Walker A motif; other site 358220002399 ATP binding site [chemical binding]; other site 358220002400 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 358220002401 Walker B motif; other site 358220002402 arginine finger; other site 358220002403 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 358220002404 cell division protein MraZ; Reviewed; Region: PRK00326 358220002405 MraZ protein; Region: MraZ; pfam02381 358220002406 MraZ protein; Region: MraZ; pfam02381 358220002407 MraW methylase family; Region: Methyltransf_5; cl17771 358220002408 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 358220002409 Cell division protein FtsL; Region: FtsL; pfam04999 358220002410 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 358220002411 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 358220002412 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 358220002413 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 358220002414 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 358220002415 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 358220002416 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 358220002417 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 358220002418 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 358220002419 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 358220002420 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 358220002421 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 358220002422 Mg++ binding site [ion binding]; other site 358220002423 putative catalytic motif [active] 358220002424 putative substrate binding site [chemical binding]; other site 358220002425 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 358220002426 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 358220002427 cell division protein FtsW; Region: ftsW; TIGR02614 358220002428 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 358220002429 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 358220002430 active site 358220002431 homodimer interface [polypeptide binding]; other site 358220002432 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 358220002433 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 358220002434 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 358220002435 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 358220002436 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 358220002437 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 358220002438 ATP-grasp domain; Region: ATP-grasp_4; cl17255 358220002439 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 358220002440 Cell division protein FtsQ; Region: FtsQ; pfam03799 358220002441 cell division protein FtsA; Region: ftsA; TIGR01174 358220002442 Cell division protein FtsA; Region: FtsA; smart00842 358220002443 Cell division protein FtsA; Region: FtsA; pfam14450 358220002444 cell division protein FtsZ; Validated; Region: PRK09330 358220002445 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 358220002446 nucleotide binding site [chemical binding]; other site 358220002447 SulA interaction site; other site 358220002448 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 358220002449 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220002450 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220002451 dimer interface [polypeptide binding]; other site 358220002452 putative CheW interface [polypeptide binding]; other site 358220002453 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 358220002454 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 358220002455 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 358220002456 ThiC-associated domain; Region: ThiC-associated; pfam13667 358220002457 ThiC family; Region: ThiC; pfam01964 358220002458 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220002459 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220002460 dimerization interface [polypeptide binding]; other site 358220002461 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220002462 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220002463 dimer interface [polypeptide binding]; other site 358220002464 putative CheW interface [polypeptide binding]; other site 358220002465 type II secretion system protein E; Region: type_II_gspE; TIGR02533 358220002466 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 358220002467 Walker A motif; other site 358220002468 ATP binding site [chemical binding]; other site 358220002469 Walker B motif; other site 358220002470 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 358220002471 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 358220002472 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 358220002473 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 358220002474 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 358220002475 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 358220002476 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 358220002477 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 358220002478 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 358220002479 Prokaryotic N-terminal methylation motif; Region: N_methyl; pfam07963 358220002480 type II secretion system protein I; Region: gspI; TIGR01707 358220002481 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 358220002482 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 358220002483 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 358220002484 cobalamin synthase; Reviewed; Region: cobS; PRK00235 358220002485 threonine dehydratase; Reviewed; Region: PRK09224 358220002486 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 358220002487 tetramer interface [polypeptide binding]; other site 358220002488 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220002489 catalytic residue [active] 358220002490 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 358220002491 putative Ile/Val binding site [chemical binding]; other site 358220002492 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 358220002493 putative Ile/Val binding site [chemical binding]; other site 358220002494 OsmC-like protein; Region: OsmC; cl00767 358220002495 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 358220002496 diiron binding motif [ion binding]; other site 358220002497 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 358220002498 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 358220002499 trimer interface [polypeptide binding]; other site 358220002500 eyelet of channel; other site 358220002501 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 358220002502 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 358220002503 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 358220002504 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220002505 dimer interface [polypeptide binding]; other site 358220002506 conserved gate region; other site 358220002507 putative PBP binding loops; other site 358220002508 ABC-ATPase subunit interface; other site 358220002509 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 358220002510 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 358220002511 metal binding site [ion binding]; metal-binding site 358220002512 putative dimer interface [polypeptide binding]; other site 358220002513 potential frameshift: common BLAST hit: gi|120609630|ref|YP_969308.1| extracellular solute-binding protein 358220002514 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 358220002515 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220002516 dimer interface [polypeptide binding]; other site 358220002517 conserved gate region; other site 358220002518 putative PBP binding loops; other site 358220002519 ABC-ATPase subunit interface; other site 358220002520 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 358220002521 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 358220002522 Walker A/P-loop; other site 358220002523 ATP binding site [chemical binding]; other site 358220002524 Q-loop/lid; other site 358220002525 ABC transporter signature motif; other site 358220002526 Walker B; other site 358220002527 D-loop; other site 358220002528 H-loop/switch region; other site 358220002529 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 358220002530 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 358220002531 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 358220002532 Walker A/P-loop; other site 358220002533 ATP binding site [chemical binding]; other site 358220002534 Q-loop/lid; other site 358220002535 ABC transporter signature motif; other site 358220002536 Walker B; other site 358220002537 D-loop; other site 358220002538 H-loop/switch region; other site 358220002539 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 358220002540 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220002541 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220002542 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220002543 putative effector binding pocket; other site 358220002544 dimerization interface [polypeptide binding]; other site 358220002545 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220002546 substrate binding site [chemical binding]; other site 358220002547 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 358220002548 oxyanion hole (OAH) forming residues; other site 358220002549 trimer interface [polypeptide binding]; other site 358220002550 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220002551 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220002552 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220002553 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 358220002554 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220002555 dimer interface [polypeptide binding]; other site 358220002556 active site 358220002557 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 358220002558 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220002559 active site 358220002560 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 358220002561 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 358220002562 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 358220002563 active site 358220002564 enoyl-CoA hydratase; Provisional; Region: PRK07511 358220002565 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220002566 substrate binding site [chemical binding]; other site 358220002567 oxyanion hole (OAH) forming residues; other site 358220002568 trimer interface [polypeptide binding]; other site 358220002569 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 358220002570 CoA-transferase family III; Region: CoA_transf_3; pfam02515 358220002571 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220002572 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220002573 AMP-binding enzyme; Region: AMP-binding; pfam00501 358220002574 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220002575 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 358220002576 acyl-activating enzyme (AAE) consensus motif; other site 358220002577 acyl-activating enzyme (AAE) consensus motif; other site 358220002578 putative AMP binding site [chemical binding]; other site 358220002579 putative active site [active] 358220002580 putative CoA binding site [chemical binding]; other site 358220002581 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 358220002582 Ligand binding site [chemical binding]; other site 358220002583 Electron transfer flavoprotein domain; Region: ETF; pfam01012 358220002584 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 358220002585 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 358220002586 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 358220002587 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220002588 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 358220002589 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 358220002590 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 358220002591 putative active site [active] 358220002592 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 358220002593 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 358220002594 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 358220002595 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220002596 dimer interface [polypeptide binding]; other site 358220002597 conserved gate region; other site 358220002598 putative PBP binding loops; other site 358220002599 ABC-ATPase subunit interface; other site 358220002600 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220002601 dimer interface [polypeptide binding]; other site 358220002602 conserved gate region; other site 358220002603 putative PBP binding loops; other site 358220002604 ABC-ATPase subunit interface; other site 358220002605 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 358220002606 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220002607 Walker A/P-loop; other site 358220002608 ATP binding site [chemical binding]; other site 358220002609 Q-loop/lid; other site 358220002610 ABC transporter signature motif; other site 358220002611 Walker B; other site 358220002612 D-loop; other site 358220002613 H-loop/switch region; other site 358220002614 TOBE domain; Region: TOBE_2; pfam08402 358220002615 transaldolase-like protein; Provisional; Region: PTZ00411 358220002616 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 358220002617 active site 358220002618 dimer interface [polypeptide binding]; other site 358220002619 catalytic residue [active] 358220002620 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 358220002621 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220002622 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220002623 dimer interface [polypeptide binding]; other site 358220002624 phosphorylation site [posttranslational modification] 358220002625 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220002626 ATP binding site [chemical binding]; other site 358220002627 Mg2+ binding site [ion binding]; other site 358220002628 G-X-G motif; other site 358220002629 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220002630 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220002631 active site 358220002632 phosphorylation site [posttranslational modification] 358220002633 intermolecular recognition site; other site 358220002634 dimerization interface [polypeptide binding]; other site 358220002635 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220002636 DNA binding site [nucleotide binding] 358220002637 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 358220002638 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 358220002639 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 358220002640 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 358220002641 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220002642 dimer interface [polypeptide binding]; other site 358220002643 conserved gate region; other site 358220002644 putative PBP binding loops; other site 358220002645 ABC-ATPase subunit interface; other site 358220002646 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 358220002647 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220002648 dimer interface [polypeptide binding]; other site 358220002649 conserved gate region; other site 358220002650 putative PBP binding loops; other site 358220002651 ABC-ATPase subunit interface; other site 358220002652 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 358220002653 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 358220002654 Walker A/P-loop; other site 358220002655 ATP binding site [chemical binding]; other site 358220002656 Q-loop/lid; other site 358220002657 ABC transporter signature motif; other site 358220002658 Walker B; other site 358220002659 D-loop; other site 358220002660 H-loop/switch region; other site 358220002661 TOBE domain; Region: TOBE_2; pfam08402 358220002662 glucokinase; Provisional; Region: glk; PRK00292 358220002663 glucokinase, proteobacterial type; Region: glk; TIGR00749 358220002664 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 358220002665 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220002666 active site 358220002667 metal binding site [ion binding]; metal-binding site 358220002668 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 358220002669 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 358220002670 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 358220002671 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 358220002672 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 358220002673 active site 358220002674 dimer interface [polypeptide binding]; other site 358220002675 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 358220002676 dimer interface [polypeptide binding]; other site 358220002677 active site 358220002678 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 358220002679 dimerization interface [polypeptide binding]; other site 358220002680 putative active cleft [active] 358220002681 Uncharacterized conserved protein [Function unknown]; Region: COG3791 358220002682 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 358220002683 phosphogluconate dehydratase; Validated; Region: PRK09054 358220002684 6-phosphogluconate dehydratase; Region: edd; TIGR01196 358220002685 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 358220002686 active site 358220002687 intersubunit interface [polypeptide binding]; other site 358220002688 catalytic residue [active] 358220002689 Protein of unknown function (DUF805); Region: DUF805; pfam05656 358220002690 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 358220002691 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 358220002692 ring oligomerisation interface [polypeptide binding]; other site 358220002693 ATP/Mg binding site [chemical binding]; other site 358220002694 stacking interactions; other site 358220002695 hinge regions; other site 358220002696 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 358220002697 oligomerisation interface [polypeptide binding]; other site 358220002698 mobile loop; other site 358220002699 roof hairpin; other site 358220002700 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 358220002701 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 358220002702 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220002703 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220002704 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220002705 dimerization interface [polypeptide binding]; other site 358220002706 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 358220002707 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 358220002708 [2Fe-2S] cluster binding site [ion binding]; other site 358220002709 PAS fold; Region: PAS_4; pfam08448 358220002710 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220002711 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 358220002712 Walker A motif; other site 358220002713 ATP binding site [chemical binding]; other site 358220002714 Walker B motif; other site 358220002715 arginine finger; other site 358220002716 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 358220002717 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 358220002718 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220002719 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 358220002720 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 358220002721 dihydropyrimidine dehydrogenase subunit B; Validated; Region: PRK08318 358220002722 Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and...; Region: DHPD_FMN; cd02940 358220002723 homodimer interface [polypeptide binding]; other site 358220002724 active site 358220002725 FMN binding site [chemical binding]; other site 358220002726 substrate binding site [chemical binding]; other site 358220002727 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 358220002728 uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily, YbbW-like; solute-binding domain; Region: SLC-NCS1sbd_YbbW-like; cd11485 358220002729 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 358220002730 Na binding site [ion binding]; other site 358220002731 putative substrate binding site [chemical binding]; other site 358220002732 phenylhydantoinase; Validated; Region: PRK08323 358220002733 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine...; Region: D-HYD; cd01314 358220002734 tetramer interface [polypeptide binding]; other site 358220002735 active site 358220002736 allantoate amidohydrolase; Reviewed; Region: PRK12893 358220002737 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 358220002738 active site 358220002739 metal binding site [ion binding]; metal-binding site 358220002740 dimer interface [polypeptide binding]; other site 358220002741 bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional; Region: PRK05379 358220002742 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 358220002743 active site 358220002744 nucleotide binding site [chemical binding]; other site 358220002745 HIGH motif; other site 358220002746 KMSKS motif; other site 358220002747 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 358220002748 nudix motif; other site 358220002749 NAD synthetase; Provisional; Region: PRK13981 358220002750 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 358220002751 multimer interface [polypeptide binding]; other site 358220002752 active site 358220002753 catalytic triad [active] 358220002754 protein interface 1 [polypeptide binding]; other site 358220002755 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 358220002756 homodimer interface [polypeptide binding]; other site 358220002757 NAD binding pocket [chemical binding]; other site 358220002758 ATP binding pocket [chemical binding]; other site 358220002759 Mg binding site [ion binding]; other site 358220002760 active-site loop [active] 358220002761 nicotinate phosphoribosyltransferase; Provisional; Region: PRK05321 358220002762 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 358220002763 active site 358220002764 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 358220002765 catalytic triad [active] 358220002766 conserved cis-peptide bond; other site 358220002767 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 358220002768 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 358220002769 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 358220002770 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220002771 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220002772 metal binding site [ion binding]; metal-binding site 358220002773 active site 358220002774 I-site; other site 358220002775 Hemerythrin-like domain; Region: Hr-like; cd12108 358220002776 S-adenosylmethionine synthetase; Validated; Region: PRK05250 358220002777 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 358220002778 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 358220002779 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 358220002780 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 358220002781 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 358220002782 putative acyl-acceptor binding pocket; other site 358220002783 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 358220002784 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 358220002785 putative acyl-acceptor binding pocket; other site 358220002786 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 358220002787 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 358220002788 G1 box; other site 358220002789 GTP/Mg2+ binding site [chemical binding]; other site 358220002790 Switch I region; other site 358220002791 G2 box; other site 358220002792 G3 box; other site 358220002793 Switch II region; other site 358220002794 G4 box; other site 358220002795 G5 box; other site 358220002796 Cytochrome c553 [Energy production and conversion]; Region: COG2863 358220002797 Cytochrome c; Region: Cytochrom_C; cl11414 358220002798 ResB-like family; Region: ResB; pfam05140 358220002799 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 358220002800 ResB-like family; Region: ResB; pfam05140 358220002801 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 358220002802 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 358220002803 TMAO/DMSO reductase; Reviewed; Region: PRK05363 358220002804 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 358220002805 Moco binding site; other site 358220002806 metal coordination site [ion binding]; other site 358220002807 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 358220002808 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 358220002809 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 358220002810 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; pfam13627 358220002811 Frataxin-like domain; Region: Frataxin_Cyay; pfam01491 358220002812 putative iron binding site [ion binding]; other site 358220002813 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 358220002814 Transglycosylase; Region: Transgly; pfam00912 358220002815 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 358220002816 Competence protein A; Region: Competence_A; pfam11104 358220002817 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 358220002818 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 358220002819 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 358220002820 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 358220002821 Pilus assembly protein, PilO; Region: PilO; pfam04350 358220002822 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 358220002823 Pilus assembly protein, PilP; Region: PilP; pfam04351 358220002824 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 358220002825 active site 358220002826 dimer interface [polypeptide binding]; other site 358220002827 metal binding site [ion binding]; metal-binding site 358220002828 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 358220002829 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220002830 Zn2+ binding site [ion binding]; other site 358220002831 Mg2+ binding site [ion binding]; other site 358220002832 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 358220002833 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 358220002834 Methyltransferase domain; Region: Methyltransf_32; pfam13679 358220002835 Methyltransferase domain; Region: Methyltransf_31; pfam13847 358220002836 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 358220002837 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 358220002838 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 358220002839 active site 358220002840 dimer interface [polypeptide binding]; other site 358220002841 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 358220002842 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 358220002843 active site 358220002844 FMN binding site [chemical binding]; other site 358220002845 substrate binding site [chemical binding]; other site 358220002846 3Fe-4S cluster binding site [ion binding]; other site 358220002847 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 358220002848 domain interface; other site 358220002849 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 358220002850 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 358220002851 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 358220002852 Walker A/P-loop; other site 358220002853 ATP binding site [chemical binding]; other site 358220002854 Q-loop/lid; other site 358220002855 ABC transporter signature motif; other site 358220002856 Walker B; other site 358220002857 D-loop; other site 358220002858 H-loop/switch region; other site 358220002859 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 358220002860 Permease; Region: Permease; pfam02405 358220002861 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 358220002862 mce related protein; Region: MCE; pfam02470 358220002863 VacJ like lipoprotein; Region: VacJ; cl01073 358220002864 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 358220002865 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 358220002866 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 358220002867 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 358220002868 Walker A/P-loop; other site 358220002869 ATP binding site [chemical binding]; other site 358220002870 Q-loop/lid; other site 358220002871 ABC transporter signature motif; other site 358220002872 Walker B; other site 358220002873 D-loop; other site 358220002874 H-loop/switch region; other site 358220002875 ABC-2 type transporter; Region: ABC2_membrane; cl17235 358220002876 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 358220002877 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 358220002878 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 358220002879 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 358220002880 hinge; other site 358220002881 active site 358220002882 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 358220002883 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 358220002884 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 358220002885 histidinol dehydrogenase; Region: hisD; TIGR00069 358220002886 NAD binding site [chemical binding]; other site 358220002887 dimerization interface [polypeptide binding]; other site 358220002888 product binding site; other site 358220002889 substrate binding site [chemical binding]; other site 358220002890 zinc binding site [ion binding]; other site 358220002891 catalytic residues [active] 358220002892 putative active site [active] 358220002893 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 358220002894 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 358220002895 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220002896 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220002897 homodimer interface [polypeptide binding]; other site 358220002898 catalytic residue [active] 358220002899 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 358220002900 putative active site pocket [active] 358220002901 4-fold oligomerization interface [polypeptide binding]; other site 358220002902 metal binding residues [ion binding]; metal-binding site 358220002903 3-fold/trimer interface [polypeptide binding]; other site 358220002904 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 358220002905 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 358220002906 putative active site [active] 358220002907 oxyanion strand; other site 358220002908 catalytic triad [active] 358220002909 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 358220002910 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 358220002911 catalytic residues [active] 358220002912 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 358220002913 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 358220002914 substrate binding site [chemical binding]; other site 358220002915 glutamase interaction surface [polypeptide binding]; other site 358220002916 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 358220002917 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 358220002918 metal binding site [ion binding]; metal-binding site 358220002919 Predicted membrane protein [Function unknown]; Region: COG3671 358220002920 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 358220002921 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 358220002922 active site 358220002923 nucleophile elbow; other site 358220002924 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 358220002925 nucleotide binding site/active site [active] 358220002926 HIT family signature motif; other site 358220002927 catalytic residue [active] 358220002928 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 358220002929 twin arginine translocase protein A; Provisional; Region: tatA; PRK00442 358220002930 sec-independent translocase; Provisional; Region: tatB; PRK01919 358220002931 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 358220002932 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 358220002933 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 358220002934 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 358220002935 protein binding site [polypeptide binding]; other site 358220002936 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 358220002937 Uncharacterized conserved protein [Function unknown]; Region: COG0327 358220002938 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 358220002939 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 358220002940 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 358220002941 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 358220002942 Rieske Fe-S protein [Energy production and conversion]; Region: QcrA; COG0723 358220002943 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 358220002944 [2Fe-2S] cluster binding site [ion binding]; other site 358220002945 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 358220002946 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 358220002947 Qi binding site; other site 358220002948 intrachain domain interface; other site 358220002949 interchain domain interface [polypeptide binding]; other site 358220002950 heme bH binding site [chemical binding]; other site 358220002951 heme bL binding site [chemical binding]; other site 358220002952 Qo binding site; other site 358220002953 interchain domain interface [polypeptide binding]; other site 358220002954 intrachain domain interface; other site 358220002955 Qi binding site; other site 358220002956 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 358220002957 Qo binding site; other site 358220002958 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 358220002959 stringent starvation protein A; Provisional; Region: sspA; PRK09481 358220002960 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 358220002961 C-terminal domain interface [polypeptide binding]; other site 358220002962 putative GSH binding site (G-site) [chemical binding]; other site 358220002963 dimer interface [polypeptide binding]; other site 358220002964 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 358220002965 dimer interface [polypeptide binding]; other site 358220002966 N-terminal domain interface [polypeptide binding]; other site 358220002967 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 358220002968 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 358220002969 Peptidase family M23; Region: Peptidase_M23; pfam01551 358220002970 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 358220002971 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 358220002972 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 358220002973 nucleotide binding region [chemical binding]; other site 358220002974 SEC-C motif; Region: SEC-C; pfam02810 358220002975 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 358220002976 heterotetramer interface [polypeptide binding]; other site 358220002977 active site pocket [active] 358220002978 cleavage site 358220002979 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 358220002980 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220002981 Walker A motif; other site 358220002982 ATP binding site [chemical binding]; other site 358220002983 Walker B motif; other site 358220002984 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 358220002985 active site 358220002986 8-oxo-dGMP binding site [chemical binding]; other site 358220002987 nudix motif; other site 358220002988 metal binding site [ion binding]; metal-binding site 358220002989 Domain of unknown function (DUF329); Region: DUF329; pfam03884 358220002990 hypothetical protein; Provisional; Region: PRK05287 358220002991 Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis; Region: DPCK; cd02022 358220002992 dephospho-CoA kinase; Region: TIGR00152 358220002993 CoA-binding site [chemical binding]; other site 358220002994 ATP-binding [chemical binding]; other site 358220002995 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 358220002996 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 358220002997 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 358220002998 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 358220002999 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 358220003000 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 358220003001 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 358220003002 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 358220003003 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 358220003004 Walker A motif; other site 358220003005 ATP binding site [chemical binding]; other site 358220003006 Walker B motif; other site 358220003007 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 358220003008 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 358220003009 substrate binding pocket [chemical binding]; other site 358220003010 chain length determination region; other site 358220003011 substrate-Mg2+ binding site; other site 358220003012 catalytic residues [active] 358220003013 aspartate-rich region 1; other site 358220003014 active site lid residues [active] 358220003015 aspartate-rich region 2; other site 358220003016 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 358220003017 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 358220003018 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 358220003019 GTPase CgtA; Reviewed; Region: obgE; PRK12299 358220003020 GTP1/OBG; Region: GTP1_OBG; pfam01018 358220003021 Obg GTPase; Region: Obg; cd01898 358220003022 G1 box; other site 358220003023 GTP/Mg2+ binding site [chemical binding]; other site 358220003024 Switch I region; other site 358220003025 G2 box; other site 358220003026 G3 box; other site 358220003027 Switch II region; other site 358220003028 G4 box; other site 358220003029 G5 box; other site 358220003030 gamma-glutamyl kinase; Provisional; Region: PRK05429 358220003031 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 358220003032 nucleotide binding site [chemical binding]; other site 358220003033 homotetrameric interface [polypeptide binding]; other site 358220003034 putative phosphate binding site [ion binding]; other site 358220003035 putative allosteric binding site; other site 358220003036 PUA domain; Region: PUA; pfam01472 358220003037 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 358220003038 putative active site [active] 358220003039 Ap4A binding site [chemical binding]; other site 358220003040 nudix motif; other site 358220003041 putative metal binding site [ion binding]; other site 358220003042 prolyl-tRNA synthetase; Provisional; Region: PRK09194 358220003043 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 358220003044 dimer interface [polypeptide binding]; other site 358220003045 motif 1; other site 358220003046 active site 358220003047 motif 2; other site 358220003048 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 358220003049 putative deacylase active site [active] 358220003050 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 358220003051 active site 358220003052 motif 3; other site 358220003053 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 358220003054 anticodon binding site; other site 358220003055 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 358220003056 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 358220003057 N-acetyl-D-glucosamine binding site [chemical binding]; other site 358220003058 catalytic residue [active] 358220003059 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 358220003060 Domain of unknown function DUF21; Region: DUF21; pfam01595 358220003061 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 358220003062 Transporter associated domain; Region: CorC_HlyC; smart01091 358220003063 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220003064 Walker A motif; other site 358220003065 ATP binding site [chemical binding]; other site 358220003066 Walker B motif; other site 358220003067 arginine finger; other site 358220003068 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 358220003069 putative GSH binding site [chemical binding]; other site 358220003070 catalytic residues [active] 358220003071 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 358220003072 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220003073 S-adenosylmethionine binding site [chemical binding]; other site 358220003074 peptide chain release factor 1; Validated; Region: prfA; PRK00591 358220003075 This domain is found in peptide chain release factors; Region: PCRF; smart00937 358220003076 RF-1 domain; Region: RF-1; pfam00472 358220003077 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 358220003078 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 358220003079 tRNA; other site 358220003080 putative tRNA binding site [nucleotide binding]; other site 358220003081 putative NADP binding site [chemical binding]; other site 358220003082 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 358220003083 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220003084 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 358220003085 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 358220003086 putative active site [active] 358220003087 catalytic site [active] 358220003088 putative metal binding site [ion binding]; other site 358220003089 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 358220003090 active site 358220003091 metal binding site [ion binding]; metal-binding site 358220003092 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220003093 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 358220003094 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 358220003095 Walker A/P-loop; other site 358220003096 ATP binding site [chemical binding]; other site 358220003097 Q-loop/lid; other site 358220003098 ABC transporter signature motif; other site 358220003099 Walker B; other site 358220003100 D-loop; other site 358220003101 H-loop/switch region; other site 358220003102 TOBE domain; Region: TOBE_2; pfam08402 358220003103 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 358220003104 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220003105 dimer interface [polypeptide binding]; other site 358220003106 conserved gate region; other site 358220003107 putative PBP binding loops; other site 358220003108 ABC-ATPase subunit interface; other site 358220003109 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220003110 dimer interface [polypeptide binding]; other site 358220003111 conserved gate region; other site 358220003112 putative PBP binding loops; other site 358220003113 ABC-ATPase subunit interface; other site 358220003114 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 358220003115 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 358220003116 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 358220003117 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 358220003118 ligand binding site [chemical binding]; other site 358220003119 NAD binding site [chemical binding]; other site 358220003120 tetramer interface [polypeptide binding]; other site 358220003121 catalytic site [active] 358220003122 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 358220003123 L-serine binding site [chemical binding]; other site 358220003124 ACT domain interface; other site 358220003125 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 358220003126 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 358220003127 FAD binding domain; Region: FAD_binding_4; pfam01565 358220003128 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 358220003129 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 358220003130 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 358220003131 Cysteine-rich domain; Region: CCG; pfam02754 358220003132 Cysteine-rich domain; Region: CCG; pfam02754 358220003133 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 358220003134 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 358220003135 HIT family signature motif; other site 358220003136 catalytic residue [active] 358220003137 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 358220003138 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 358220003139 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220003140 S-adenosylmethionine binding site [chemical binding]; other site 358220003141 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 358220003142 SCP-2 sterol transfer family; Region: SCP2; pfam02036 358220003143 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 358220003144 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 358220003145 potential frameshift: common BLAST hit: gi|264676933|ref|YP_003276839.1| Na+/solute symporter 358220003146 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 358220003147 Uncharacterized conserved protein [Function unknown]; Region: COG2928 358220003148 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 358220003149 EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND)...; Region: EcAspRS_like_N; cd04317 358220003150 dimer interface [polypeptide binding]; other site 358220003151 anticodon binding site; other site 358220003152 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 358220003153 homodimer interface [polypeptide binding]; other site 358220003154 motif 1; other site 358220003155 active site 358220003156 motif 2; other site 358220003157 GAD domain; Region: GAD; pfam02938 358220003158 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 358220003159 motif 3; other site 358220003160 Curli production assembly/transport component CsgG; Region: CsgG; cl17434 358220003161 dihydroneopterin triphosphate pyrophosphatase; Provisional; Region: nudB; PRK09438 358220003162 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220003163 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220003164 active site 358220003165 phosphorylation site [posttranslational modification] 358220003166 intermolecular recognition site; other site 358220003167 dimerization interface [polypeptide binding]; other site 358220003168 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 358220003169 binding surface 358220003170 TPR motif; other site 358220003171 Tetratricopeptide repeat; Region: TPR_16; pfam13432 358220003172 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 358220003173 putative catalytic site [active] 358220003174 putative metal binding site [ion binding]; other site 358220003175 putative phosphate binding site [ion binding]; other site 358220003176 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 358220003177 putative active site [active] 358220003178 catalytic site [active] 358220003179 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 358220003180 PLD-like domain; Region: PLDc_2; pfam13091 358220003181 putative active site [active] 358220003182 catalytic site [active] 358220003183 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 358220003184 active site 358220003185 Sensors of blue-light using FAD; Region: BLUF; smart01034 358220003186 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 358220003187 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 358220003188 catalytic core [active] 358220003189 StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been...; Region: StaR_like; cd05804 358220003190 amidase; Provisional; Region: PRK07042 358220003191 Amidase; Region: Amidase; cl11426 358220003192 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 358220003193 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_6; cd08494 358220003194 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 358220003195 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 358220003196 Walker A/P-loop; other site 358220003197 ATP binding site [chemical binding]; other site 358220003198 Q-loop/lid; other site 358220003199 ABC transporter signature motif; other site 358220003200 Walker B; other site 358220003201 D-loop; other site 358220003202 H-loop/switch region; other site 358220003203 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 358220003204 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 358220003205 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 358220003206 Walker A/P-loop; other site 358220003207 ATP binding site [chemical binding]; other site 358220003208 Q-loop/lid; other site 358220003209 ABC transporter signature motif; other site 358220003210 Walker B; other site 358220003211 D-loop; other site 358220003212 H-loop/switch region; other site 358220003213 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 358220003214 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 358220003215 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220003216 dimer interface [polypeptide binding]; other site 358220003217 conserved gate region; other site 358220003218 putative PBP binding loops; other site 358220003219 ABC-ATPase subunit interface; other site 358220003220 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 358220003221 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220003222 dimer interface [polypeptide binding]; other site 358220003223 conserved gate region; other site 358220003224 putative PBP binding loops; other site 358220003225 ABC-ATPase subunit interface; other site 358220003226 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 358220003227 Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through...; Region: PTH; cd00462 358220003228 putative active site [active] 358220003229 catalytic residue [active] 358220003230 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 358220003231 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 358220003232 5S rRNA interface [nucleotide binding]; other site 358220003233 CTC domain interface [polypeptide binding]; other site 358220003234 L16 interface [polypeptide binding]; other site 358220003235 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 358220003236 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 358220003237 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220003238 active site 358220003239 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 358220003240 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 358220003241 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 358220003242 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 358220003243 binding surface 358220003244 TPR motif; other site 358220003245 TPR repeat; Region: TPR_11; pfam13414 358220003246 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 358220003247 Formamidopyrimidine-DNA glycosylase N-terminal domain; Region: Fapy_DNA_glyco; smart00898 358220003248 DNA binding site [nucleotide binding] 358220003249 catalytic residue [active] 358220003250 H2TH interface [polypeptide binding]; other site 358220003251 putative catalytic residues [active] 358220003252 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 358220003253 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 358220003254 Dynamin family; Region: Dynamin_N; pfam00350 358220003255 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 358220003256 G1 box; other site 358220003257 GTP/Mg2+ binding site [chemical binding]; other site 358220003258 G2 box; other site 358220003259 Switch I region; other site 358220003260 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 358220003261 G3 box; other site 358220003262 Switch II region; other site 358220003263 GTP/Mg2+ binding site [chemical binding]; other site 358220003264 G4 box; other site 358220003265 G5 box; other site 358220003266 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 358220003267 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 358220003268 minor groove reading motif; other site 358220003269 helix-hairpin-helix signature motif; other site 358220003270 substrate binding pocket [chemical binding]; other site 358220003271 active site 358220003272 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 358220003273 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 358220003274 DNA binding and oxoG recognition site [nucleotide binding] 358220003275 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 358220003276 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 358220003277 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 358220003278 Walker A/P-loop; other site 358220003279 ATP binding site [chemical binding]; other site 358220003280 Q-loop/lid; other site 358220003281 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 358220003282 ABC transporter signature motif; other site 358220003283 Walker B; other site 358220003284 D-loop; other site 358220003285 H-loop/switch region; other site 358220003286 NAD(+)/NADH kinase family protein; Provisional; Region: ppnK; PRK02155 358220003287 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 358220003288 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 358220003289 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 358220003290 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 358220003291 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 358220003292 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 358220003293 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 358220003294 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220003295 Zn2+ binding site [ion binding]; other site 358220003296 Mg2+ binding site [ion binding]; other site 358220003297 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 358220003298 synthetase active site [active] 358220003299 NTP binding site [chemical binding]; other site 358220003300 metal binding site [ion binding]; metal-binding site 358220003301 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 358220003302 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 358220003303 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 358220003304 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 358220003305 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 358220003306 catalytic site [active] 358220003307 G-X2-G-X-G-K; other site 358220003308 hypothetical protein; Provisional; Region: PRK11820 358220003309 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 358220003310 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 358220003311 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 358220003312 Catalytic domain of Protein Kinases; Region: PKc; cd00180 358220003313 active site 358220003314 ATP binding site [chemical binding]; other site 358220003315 substrate binding site [chemical binding]; other site 358220003316 activation loop (A-loop); other site 358220003317 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 358220003318 Protein phosphatase 2C; Region: PP2C; pfam00481 358220003319 active site 358220003320 ribonuclease PH; Reviewed; Region: rph; PRK00173 358220003321 Ribonuclease PH; Region: RNase_PH_bact; cd11362 358220003322 hexamer interface [polypeptide binding]; other site 358220003323 active site 358220003324 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 358220003325 active site 358220003326 dimerization interface [polypeptide binding]; other site 358220003327 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 358220003328 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220003329 FeS/SAM binding site; other site 358220003330 HemN C-terminal domain; Region: HemN_C; pfam06969 358220003331 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 358220003332 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 358220003333 PAS fold; Region: PAS_7; pfam12860 358220003334 PAS fold; Region: PAS_7; pfam12860 358220003335 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220003336 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220003337 metal binding site [ion binding]; metal-binding site 358220003338 active site 358220003339 I-site; other site 358220003340 Homeodomain-like domain; Region: HTH_23; cl17451 358220003341 putative transposase OrfB; Reviewed; Region: PHA02517 358220003342 Integrase core domain; Region: rve; pfam00665 358220003343 Integrase core domain; Region: rve_3; pfam13683 358220003344 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cl00787 358220003345 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 358220003346 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 358220003347 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 358220003348 Beta-lactamase; Region: Beta-lactamase; pfam00144 358220003349 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 358220003350 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 358220003351 UreF; Region: UreF; pfam01730 358220003352 urease accessory protein UreE; Provisional; Region: ureE; PRK13263 358220003353 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 358220003354 dimer interface [polypeptide binding]; other site 358220003355 catalytic residues [active] 358220003356 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220003357 Coenzyme A binding pocket [chemical binding]; other site 358220003358 urease subunit alpha; Reviewed; Region: ureC; PRK13207 358220003359 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 358220003360 subunit interactions [polypeptide binding]; other site 358220003361 active site 358220003362 flap region; other site 358220003363 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 358220003364 gamma-beta subunit interface [polypeptide binding]; other site 358220003365 alpha-beta subunit interface [polypeptide binding]; other site 358220003366 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 358220003367 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 358220003368 alpha-gamma subunit interface [polypeptide binding]; other site 358220003369 beta-gamma subunit interface [polypeptide binding]; other site 358220003370 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 358220003371 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220003372 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220003373 dimer interface [polypeptide binding]; other site 358220003374 phosphorylation site [posttranslational modification] 358220003375 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220003376 ATP binding site [chemical binding]; other site 358220003377 Mg2+ binding site [ion binding]; other site 358220003378 G-X-G motif; other site 358220003379 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220003380 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220003381 active site 358220003382 phosphorylation site [posttranslational modification] 358220003383 intermolecular recognition site; other site 358220003384 dimerization interface [polypeptide binding]; other site 358220003385 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220003386 active site 358220003387 phosphorylation site [posttranslational modification] 358220003388 intermolecular recognition site; other site 358220003389 dimerization interface [polypeptide binding]; other site 358220003390 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220003391 DNA binding residues [nucleotide binding] 358220003392 dimerization interface [polypeptide binding]; other site 358220003393 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 358220003394 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 358220003395 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220003396 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 358220003397 Soluble P-type ATPase [General function prediction only]; Region: COG4087 358220003398 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 358220003399 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 358220003400 Protein of unknown function (DUF917); Region: DUF917; cl17829 358220003401 PAS fold; Region: PAS_3; pfam08447 358220003402 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220003403 putative active site [active] 358220003404 heme pocket [chemical binding]; other site 358220003405 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220003406 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220003407 metal binding site [ion binding]; metal-binding site 358220003408 active site 358220003409 I-site; other site 358220003410 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 358220003411 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 358220003412 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 358220003413 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 358220003414 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 358220003415 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220003416 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220003417 MFS transport protein AraJ; Provisional; Region: PRK10091 358220003418 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220003419 putative substrate translocation pore; other site 358220003420 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220003421 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 358220003422 putative ligand binding site [chemical binding]; other site 358220003423 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220003424 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220003425 TM-ABC transporter signature motif; other site 358220003426 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220003427 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220003428 TM-ABC transporter signature motif; other site 358220003429 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 358220003430 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220003431 Walker A/P-loop; other site 358220003432 ATP binding site [chemical binding]; other site 358220003433 Q-loop/lid; other site 358220003434 ABC transporter signature motif; other site 358220003435 Walker B; other site 358220003436 D-loop; other site 358220003437 H-loop/switch region; other site 358220003438 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 358220003439 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220003440 Walker A/P-loop; other site 358220003441 ATP binding site [chemical binding]; other site 358220003442 Q-loop/lid; other site 358220003443 ABC transporter signature motif; other site 358220003444 Walker B; other site 358220003445 D-loop; other site 358220003446 H-loop/switch region; other site 358220003447 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 358220003448 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 358220003449 active site 358220003450 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 358220003451 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 358220003452 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 358220003453 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 358220003454 putative active site [active] 358220003455 putative metal binding site [ion binding]; other site 358220003456 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 358220003457 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 358220003458 cyclase homology domain; Region: CHD; cd07302 358220003459 nucleotidyl binding site; other site 358220003460 metal binding site [ion binding]; metal-binding site 358220003461 dimer interface [polypeptide binding]; other site 358220003462 PilZ domain; Region: PilZ; pfam07238 358220003463 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 358220003464 Haloacid dehalogenase superfamily, subfamily IA, variant 2 with 3rd motif like haloacid dehalogenase; Region: HAD-SF-IA-v2; TIGR01493 358220003465 aminotransferase; Validated; Region: PRK08175 358220003466 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220003467 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220003468 homodimer interface [polypeptide binding]; other site 358220003469 catalytic residue [active] 358220003470 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 358220003471 nucleotide binding site [chemical binding]; other site 358220003472 UreD urease accessory protein; Region: UreD; pfam01774 358220003473 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 358220003474 FAD binding domain; Region: FAD_binding_4; pfam01565 358220003475 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 358220003476 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220003477 dimer interface [polypeptide binding]; other site 358220003478 conserved gate region; other site 358220003479 putative PBP binding loops; other site 358220003480 ABC-ATPase subunit interface; other site 358220003481 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 358220003482 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 358220003483 Walker A/P-loop; other site 358220003484 ATP binding site [chemical binding]; other site 358220003485 Q-loop/lid; other site 358220003486 ABC transporter signature motif; other site 358220003487 Walker B; other site 358220003488 D-loop; other site 358220003489 H-loop/switch region; other site 358220003490 NMT1/THI5 like; Region: NMT1; pfam09084 358220003491 Creatinine amidohydrolase; Region: Creatininase; pfam02633 358220003492 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 358220003493 homotrimer interaction site [polypeptide binding]; other site 358220003494 putative active site [active] 358220003495 cytosine deaminase-like protein; Validated; Region: PRK07583 358220003496 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi; Region: Bact_CD; cd01293 358220003497 active site 358220003498 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 358220003499 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 358220003500 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220003501 catalytic loop [active] 358220003502 iron binding site [ion binding]; other site 358220003503 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 358220003504 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220003505 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 358220003506 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 358220003507 nucleoside/Zn binding site; other site 358220003508 dimer interface [polypeptide binding]; other site 358220003509 catalytic motif [active] 358220003510 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 358220003511 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 358220003512 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 358220003513 Glyoxalase-like domain; Region: Glyoxalase_2; pfam12681 358220003514 active site 358220003515 potential frameshift: common BLAST hit: gi|300309800|ref|YP_003773892.1| isopenicillin N synthase 358220003516 NMT1/THI5 like; Region: NMT1; pfam09084 358220003517 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 358220003518 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 358220003519 hypothetical protein; Provisional; Region: PRK06489 358220003520 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 358220003521 putative aldolase; Validated; Region: PRK08130 358220003522 intersubunit interface [polypeptide binding]; other site 358220003523 active site 358220003524 Zn2+ binding site [ion binding]; other site 358220003525 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3395 358220003526 2-hydroxy-3-oxopropionate reductase; Region: tartro_sem_red; TIGR01505 358220003527 GntP family permease; Region: GntP_permease; pfam02447 358220003528 putative transporter; Provisional; Region: PRK09821 358220003529 Transcriptional regulators [Transcription]; Region: FadR; COG2186 358220003530 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220003531 DNA-binding site [nucleotide binding]; DNA binding site 358220003532 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 358220003533 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 358220003534 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 358220003535 nucleophile elbow; other site 358220003536 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 358220003537 active site 358220003538 Zn binding site [ion binding]; other site 358220003539 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 358220003540 active site 358220003541 Zn binding site [ion binding]; other site 358220003542 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 358220003543 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220003544 dimer interface [polypeptide binding]; other site 358220003545 conserved gate region; other site 358220003546 putative PBP binding loops; other site 358220003547 ABC-ATPase subunit interface; other site 358220003548 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 358220003549 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 358220003550 Walker A/P-loop; other site 358220003551 ATP binding site [chemical binding]; other site 358220003552 Q-loop/lid; other site 358220003553 ABC transporter signature motif; other site 358220003554 Walker B; other site 358220003555 D-loop; other site 358220003556 H-loop/switch region; other site 358220003557 NMT1/THI5 like; Region: NMT1; pfam09084 358220003558 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 358220003559 malic enzyme; Reviewed; Region: PRK12862 358220003560 Malic enzyme, N-terminal domain; Region: malic; pfam00390 358220003561 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 358220003562 putative NAD(P) binding site [chemical binding]; other site 358220003563 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 358220003564 xanthine permease; Region: pbuX; TIGR03173 358220003565 Transcriptional regulators [Transcription]; Region: FadR; COG2186 358220003566 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220003567 DNA-binding site [nucleotide binding]; DNA binding site 358220003568 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 358220003569 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK13027 358220003570 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 358220003571 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 358220003572 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 358220003573 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK08651 358220003574 M20 Zn-peptidases include exopeptidases; Region: M20_like; cd02697 358220003575 putative metal binding site [ion binding]; other site 358220003576 putative bifunctional OHCU decarboxylase/allantoate amidohydrolase; Provisional; Region: PRK13590 358220003577 OHCU decarboxylase; Region: OHCU_decarbox; pfam09349 358220003578 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 358220003579 active site 358220003580 metal binding site [ion binding]; metal-binding site 358220003581 dimer interface [polypeptide binding]; other site 358220003582 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 358220003583 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 358220003584 active site 358220003585 catalytic site [active] 358220003586 tetramer interface [polypeptide binding]; other site 358220003587 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220003588 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220003589 DNA-binding site [nucleotide binding]; DNA binding site 358220003590 FCD domain; Region: FCD; pfam07729 358220003591 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 358220003592 active site 358220003593 homotetramer interface [polypeptide binding]; other site 358220003594 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 358220003595 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 358220003596 XdhC Rossmann domain; Region: XdhC_C; pfam13478 358220003597 Predicted membrane protein [Function unknown]; Region: COG3748 358220003598 Protein of unknown function (DUF989); Region: DUF989; pfam06181 358220003599 Cytochrome c; Region: Cytochrom_C; pfam00034 358220003600 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220003601 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 358220003602 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220003603 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220003604 metal binding site [ion binding]; metal-binding site 358220003605 active site 358220003606 I-site; other site 358220003607 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 358220003608 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 358220003609 MOFRL family; Region: MOFRL; pfam05161 358220003610 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 358220003611 trimer interface [polypeptide binding]; other site 358220003612 eyelet of channel; other site 358220003613 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 358220003614 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220003615 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 358220003616 ligand binding site [chemical binding]; other site 358220003617 flexible hinge region; other site 358220003618 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 358220003619 putative switch regulator; other site 358220003620 non-specific DNA interactions [nucleotide binding]; other site 358220003621 DNA binding site [nucleotide binding] 358220003622 sequence specific DNA binding site [nucleotide binding]; other site 358220003623 putative cAMP binding site [chemical binding]; other site 358220003624 PAS domain; Region: PAS_9; pfam13426 358220003625 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220003626 putative active site [active] 358220003627 heme pocket [chemical binding]; other site 358220003628 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220003629 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220003630 metal binding site [ion binding]; metal-binding site 358220003631 active site 358220003632 I-site; other site 358220003633 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 358220003634 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 358220003635 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220003636 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 358220003637 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 358220003638 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 358220003639 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 358220003640 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220003641 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220003642 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220003643 dimerization interface [polypeptide binding]; other site 358220003644 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 358220003645 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 358220003646 Walker A/P-loop; other site 358220003647 ATP binding site [chemical binding]; other site 358220003648 Q-loop/lid; other site 358220003649 ABC transporter signature motif; other site 358220003650 Walker B; other site 358220003651 D-loop; other site 358220003652 H-loop/switch region; other site 358220003653 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 358220003654 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220003655 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 358220003656 TM-ABC transporter signature motif; other site 358220003657 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220003658 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 358220003659 TM-ABC transporter signature motif; other site 358220003660 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 358220003661 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 358220003662 putative ligand binding site [chemical binding]; other site 358220003663 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 358220003664 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 358220003665 [2Fe-2S] cluster binding site [ion binding]; other site 358220003666 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 358220003667 hydrophobic ligand binding site; other site 358220003668 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 358220003669 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 358220003670 active site 358220003671 purine riboside binding site [chemical binding]; other site 358220003672 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 358220003673 HIT family signature motif; other site 358220003674 catalytic residue [active] 358220003675 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 358220003676 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 358220003677 putative ligand binding site [chemical binding]; other site 358220003678 guanine deaminase; Provisional; Region: PRK09228 358220003679 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 358220003680 active site 358220003681 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 358220003682 trimer interface [polypeptide binding]; other site 358220003683 active site 358220003684 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220003685 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220003686 metal binding site [ion binding]; metal-binding site 358220003687 active site 358220003688 I-site; other site 358220003689 ornithine cyclodeaminase; Validated; Region: PRK07340 358220003690 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 358220003691 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 358220003692 putative substrate binding pocket [chemical binding]; other site 358220003693 AC domain interface; other site 358220003694 catalytic triad [active] 358220003695 AB domain interface; other site 358220003696 interchain disulfide; other site 358220003697 Predicted metalloprotease [General function prediction only]; Region: COG2321 358220003698 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 358220003699 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 358220003700 Sulfate transporter family; Region: Sulfate_transp; pfam00916 358220003701 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 358220003702 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 358220003703 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220003704 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220003705 ligand binding site [chemical binding]; other site 358220003706 flexible hinge region; other site 358220003707 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 358220003708 apolar tunnel; other site 358220003709 heme binding site [chemical binding]; other site 358220003710 dimerization interface [polypeptide binding]; other site 358220003711 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 358220003712 Peptidase family M48; Region: Peptidase_M48; cl12018 358220003713 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 358220003714 homotrimer interaction site [polypeptide binding]; other site 358220003715 putative active site [active] 358220003716 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; pfam04828 358220003717 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 358220003718 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 358220003719 active site 358220003720 metal binding site [ion binding]; metal-binding site 358220003721 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 358220003722 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 358220003723 Smr domain; Region: Smr; pfam01713 358220003724 hypothetical protein; Reviewed; Region: PRK00024 358220003725 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 358220003726 MPN+ (JAMM) motif; other site 358220003727 Zinc-binding site [ion binding]; other site 358220003728 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 358220003729 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 358220003730 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 358220003731 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 358220003732 FOG: CBS domain [General function prediction only]; Region: COG0517 358220003733 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 358220003734 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 358220003735 threonine dehydratase; Provisional; Region: PRK08246 358220003736 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220003737 catalytic residue [active] 358220003738 seryl-tRNA synthetase; Provisional; Region: PRK05431 358220003739 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 358220003740 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 358220003741 dimer interface [polypeptide binding]; other site 358220003742 active site 358220003743 motif 1; other site 358220003744 motif 2; other site 358220003745 motif 3; other site 358220003746 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 358220003747 DNA binding residues [nucleotide binding] 358220003748 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 358220003749 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 358220003750 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 358220003751 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 358220003752 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 358220003753 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 358220003754 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 358220003755 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220003756 active site 358220003757 phosphorylation site [posttranslational modification] 358220003758 intermolecular recognition site; other site 358220003759 dimerization interface [polypeptide binding]; other site 358220003760 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220003761 DNA binding site [nucleotide binding] 358220003762 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 358220003763 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220003764 dimerization interface [polypeptide binding]; other site 358220003765 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220003766 dimer interface [polypeptide binding]; other site 358220003767 phosphorylation site [posttranslational modification] 358220003768 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220003769 ATP binding site [chemical binding]; other site 358220003770 Mg2+ binding site [ion binding]; other site 358220003771 G-X-G motif; other site 358220003772 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 358220003773 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 358220003774 putative transcriptional regulator MerR; Provisional; Region: PRK13752 358220003775 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 358220003776 DNA binding residues [nucleotide binding] 358220003777 dimer interface [polypeptide binding]; other site 358220003778 mercury binding site [ion binding]; other site 358220003779 putative mercuric transport protein; Provisional; Region: PRK13751 358220003780 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220003781 metal-binding site [ion binding] 358220003782 putative mercuric reductase; Provisional; Region: PRK13748 358220003783 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220003784 metal-binding site [ion binding] 358220003785 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220003786 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 358220003787 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 358220003788 YHS domain; Region: YHS; pfam04945 358220003789 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 358220003790 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220003791 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220003792 motif II; other site 358220003793 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 358220003794 dimer interface [polypeptide binding]; other site 358220003795 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220003796 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 358220003797 ligand binding site [chemical binding]; other site 358220003798 flexible hinge region; other site 358220003799 potential frameshift: common BLAST hit: gi|121593849|ref|YP_985745.1| heavy metal sensor signal transduction histidine kinase 358220003800 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 358220003801 Integrase core domain; Region: rve_3; cl15866 358220003802 Cation efflux family; Region: Cation_efflux; cl00316 358220003803 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 358220003804 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 358220003805 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 358220003806 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 358220003807 DsbD alpha interface [polypeptide binding]; other site 358220003808 catalytic residues [active] 358220003809 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 358220003810 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 358220003811 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 358220003812 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 358220003813 homodimer interface [polypeptide binding]; other site 358220003814 NAD binding pocket [chemical binding]; other site 358220003815 ATP binding pocket [chemical binding]; other site 358220003816 Mg binding site [ion binding]; other site 358220003817 active-site loop [active] 358220003818 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 358220003819 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 358220003820 DNA binding residues [nucleotide binding] 358220003821 dimer interface [polypeptide binding]; other site 358220003822 putative metal binding site [ion binding]; other site 358220003823 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220003824 metal-binding site [ion binding] 358220003825 Heavy-metal-associated domain; Region: HMA; pfam00403 358220003826 metal-binding site [ion binding] 358220003827 Heavy-metal-associated domain; Region: HMA; pfam00403 358220003828 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 358220003829 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220003830 metal-binding site [ion binding] 358220003831 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220003832 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 358220003833 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 358220003834 active site 358220003835 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 358220003836 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 358220003837 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 358220003838 catalytic residues [active] 358220003839 Outer membrane efflux protein; Region: OEP; pfam02321 358220003840 Outer membrane efflux protein; Region: OEP; pfam02321 358220003841 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 358220003842 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220003843 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 358220003844 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 358220003845 Uncharacterized conserved protein [Function unknown]; Region: COG3339 358220003846 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 358220003847 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 358220003848 putative metal binding site [ion binding]; other site 358220003849 putative homodimer interface [polypeptide binding]; other site 358220003850 putative homotetramer interface [polypeptide binding]; other site 358220003851 putative homodimer-homodimer interface [polypeptide binding]; other site 358220003852 putative allosteric switch controlling residues; other site 358220003853 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 358220003854 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 358220003855 Nitrogen regulatory protein P-II; Region: P-II; smart00938 358220003856 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220003857 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 358220003858 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220003859 Outer membrane efflux protein; Region: OEP; pfam02321 358220003860 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 358220003861 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220003862 active site 358220003863 phosphorylation site [posttranslational modification] 358220003864 intermolecular recognition site; other site 358220003865 dimerization interface [polypeptide binding]; other site 358220003866 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220003867 DNA binding site [nucleotide binding] 358220003868 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 358220003869 HAMP domain; Region: HAMP; pfam00672 358220003870 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220003871 dimer interface [polypeptide binding]; other site 358220003872 phosphorylation site [posttranslational modification] 358220003873 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220003874 ATP binding site [chemical binding]; other site 358220003875 Mg2+ binding site [ion binding]; other site 358220003876 G-X-G motif; other site 358220003877 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220003878 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220003879 putative substrate translocation pore; other site 358220003880 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 358220003881 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220003882 dimerization interface [polypeptide binding]; other site 358220003883 putative DNA binding site [nucleotide binding]; other site 358220003884 putative Zn2+ binding site [ion binding]; other site 358220003885 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 358220003886 active site residue [active] 358220003887 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220003888 metal-binding site [ion binding] 358220003889 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 358220003890 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 358220003891 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases; Region: INT_SG5; cd01190 358220003892 Int/Topo IB signature motif; other site 358220003893 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220003894 active site 358220003895 DNA binding site [nucleotide binding] 358220003896 Int/Topo IB signature motif; other site 358220003897 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 358220003898 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220003899 active site 358220003900 DNA binding site [nucleotide binding] 358220003901 Int/Topo IB signature motif; other site 358220003902 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 358220003903 sulfite oxidase; Provisional; Region: PLN00177 358220003904 Subgroup of sulfite oxidase (SO) family molybdopterin binding domains that contains conserved dimerization domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate...; Region: SO_family_Moco_dimer; cd02110 358220003905 Moco binding site; other site 358220003906 metal coordination site [ion binding]; other site 358220003907 dimerization interface [polypeptide binding]; other site 358220003908 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220003909 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 358220003910 DNA binding residues [nucleotide binding] 358220003911 Domain of unknown function (DUF305); Region: DUF305; cl17794 358220003912 Uncharacterized conserved protein [Function unknown]; Region: COG3391 358220003913 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 358220003914 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 358220003915 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220003916 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 358220003917 DNA binding residues [nucleotide binding] 358220003918 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 358220003919 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 358220003920 SnoaL-like domain; Region: SnoaL_2; pfam12680 358220003921 Conserved hypothetical protein 698; Region: Cons_hypoth698; pfam03601 358220003922 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 358220003923 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220003924 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 358220003925 putative dimerization interface [polypeptide binding]; other site 358220003926 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 358220003927 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220003928 active site 358220003929 DNA binding site [nucleotide binding] 358220003930 Int/Topo IB signature motif; other site 358220003931 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220003932 active site 358220003933 DNA binding site [nucleotide binding] 358220003934 Int/Topo IB signature motif; other site 358220003935 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 358220003936 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 358220003937 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases; Region: INT_SG5; cd01190 358220003938 Int/Topo IB signature motif; other site 358220003939 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 358220003940 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 358220003941 protein binding site [polypeptide binding]; other site 358220003942 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 358220003943 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 358220003944 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases; Region: INT_SG5; cd01190 358220003945 Int/Topo IB signature motif; other site 358220003946 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220003947 active site 358220003948 DNA binding site [nucleotide binding] 358220003949 Int/Topo IB signature motif; other site 358220003950 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 358220003951 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220003952 active site 358220003953 DNA binding site [nucleotide binding] 358220003954 Int/Topo IB signature motif; other site 358220003955 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220003956 active site 358220003957 Predicted membrane protein [Function unknown]; Region: COG3174 358220003958 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 358220003959 glyceraldehyde-3-phosphate dehydrogenase; Provisional; Region: PRK04207 358220003960 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 358220003961 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 358220003962 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 358220003963 ABC1 family; Region: ABC1; cl17513 358220003964 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 358220003965 D-Lactate and related Dehydrogenase like proteins, NAD-binding and catalytic domains; Region: LDH_like_1; cd12187 358220003966 ligand binding site [chemical binding]; other site 358220003967 NAD binding site [chemical binding]; other site 358220003968 homodimer interface [polypeptide binding]; other site 358220003969 catalytic site [active] 358220003970 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK07199 358220003971 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 358220003972 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220003973 active site 358220003974 thymidine phosphorylase; Provisional; Region: PRK04350 358220003975 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 358220003976 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 358220003977 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 358220003978 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 358220003979 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 358220003980 Beta-Casp domain; Region: Beta-Casp; smart01027 358220003981 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 358220003982 Repair protein; Region: Repair_PSII; pfam04536 358220003983 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 358220003984 Repair protein; Region: Repair_PSII; pfam04536 358220003985 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 358220003986 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220003987 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220003988 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 358220003989 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220003990 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220003991 motif II; other site 358220003992 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 358220003993 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 358220003994 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 358220003995 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 358220003996 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 358220003997 DNA binding residues [nucleotide binding] 358220003998 dimer interface [polypeptide binding]; other site 358220003999 mercury binding site [ion binding]; other site 358220004000 Transposase domain (DUF772); Region: DUF772; pfam05598 358220004001 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 358220004002 DDE superfamily endonuclease; Region: DDE_4; cl17710 358220004003 Domain of unknown function (DUF305); Region: DUF305; pfam03713 358220004004 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 358220004005 dimerization interface [polypeptide binding]; other site 358220004006 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 358220004007 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 358220004008 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 358220004009 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 358220004010 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 358220004011 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220004012 dimerization interface [polypeptide binding]; other site 358220004013 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220004014 dimer interface [polypeptide binding]; other site 358220004015 phosphorylation site [posttranslational modification] 358220004016 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220004017 ATP binding site [chemical binding]; other site 358220004018 Mg2+ binding site [ion binding]; other site 358220004019 G-X-G motif; other site 358220004020 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 358220004021 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220004022 active site 358220004023 phosphorylation site [posttranslational modification] 358220004024 intermolecular recognition site; other site 358220004025 dimerization interface [polypeptide binding]; other site 358220004026 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220004027 DNA binding site [nucleotide binding] 358220004028 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 358220004029 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 358220004030 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 358220004031 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 358220004032 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 358220004033 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 358220004034 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 358220004035 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 358220004036 Multicopper oxidase; Region: Cu-oxidase; pfam00394 358220004037 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 358220004038 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 358220004039 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 358220004040 putative transposase OrfB; Reviewed; Region: PHA02517 358220004041 HTH-like domain; Region: HTH_21; pfam13276 358220004042 Integrase core domain; Region: rve; pfam00665 358220004043 Integrase core domain; Region: rve_2; pfam13333 358220004044 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220004045 Homeodomain-like domain; Region: HTH_23; cl17451 358220004046 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220004047 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220004048 metal-binding site [ion binding] 358220004049 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220004050 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 358220004051 metal-binding site [ion binding] 358220004052 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220004053 Soluble P-type ATPase [General function prediction only]; Region: COG4087 358220004054 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 358220004055 HAMP domain; Region: HAMP; pfam00672 358220004056 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220004057 dimer interface [polypeptide binding]; other site 358220004058 phosphorylation site [posttranslational modification] 358220004059 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220004060 ATP binding site [chemical binding]; other site 358220004061 Mg2+ binding site [ion binding]; other site 358220004062 G-X-G motif; other site 358220004063 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 358220004064 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220004065 active site 358220004066 phosphorylation site [posttranslational modification] 358220004067 intermolecular recognition site; other site 358220004068 dimerization interface [polypeptide binding]; other site 358220004069 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220004070 DNA binding site [nucleotide binding] 358220004071 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 358220004072 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220004073 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 358220004074 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220004075 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 358220004076 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 358220004077 potential frameshift: common BLAST hit: gi|91788365|ref|YP_549317.1| manganese and iron superoxide dismutase 358220004078 Chromate resistance exported protein; Region: Chrome_Resist; pfam09828 358220004079 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 358220004080 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 358220004081 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220004082 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 358220004083 integrase; Provisional; Region: PRK09692 358220004084 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 358220004085 active site 358220004086 Int/Topo IB signature motif; other site 358220004087 integrase; Provisional; Region: PRK09692 358220004088 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 358220004089 active site 358220004090 Int/Topo IB signature motif; other site 358220004091 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 358220004092 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 358220004093 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 358220004094 active site 358220004095 metal binding site [ion binding]; metal-binding site 358220004096 interdomain interaction site; other site 358220004097 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 358220004098 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 358220004099 oligomer interface [polypeptide binding]; other site 358220004100 active site residues [active] 358220004101 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 358220004102 selenophosphate synthetase; Provisional; Region: PRK00943 358220004103 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 358220004104 dimerization interface [polypeptide binding]; other site 358220004105 putative ATP binding site [chemical binding]; other site 358220004106 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 358220004107 Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB; Region: RHOD_YbbB; cd01520 358220004108 active site residue [active] 358220004109 CHASE2 domain; Region: CHASE2; pfam05226 358220004110 PAS domain; Region: PAS; smart00091 358220004111 putative active site [active] 358220004112 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220004113 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 358220004114 dimer interface [polypeptide binding]; other site 358220004115 phosphorylation site [posttranslational modification] 358220004116 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220004117 Mg2+ binding site [ion binding]; other site 358220004118 G-X-G motif; other site 358220004119 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 358220004120 FecR protein; Region: FecR; pfam04773 358220004121 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220004122 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220004123 active site 358220004124 phosphorylation site [posttranslational modification] 358220004125 intermolecular recognition site; other site 358220004126 dimerization interface [polypeptide binding]; other site 358220004127 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220004128 DNA binding site [nucleotide binding] 358220004129 Uncharacterized conserved protein [Function unknown]; Region: COG1262 358220004130 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 358220004131 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 358220004132 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 358220004133 active site 358220004134 HIGH motif; other site 358220004135 dimer interface [polypeptide binding]; other site 358220004136 KMSKS motif; other site 358220004137 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 358220004138 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 358220004139 Peptidase family M50; Region: Peptidase_M50; pfam02163 358220004140 active site 358220004141 putative substrate binding region [chemical binding]; other site 358220004142 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220004143 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220004144 dimer interface [polypeptide binding]; other site 358220004145 putative CheW interface [polypeptide binding]; other site 358220004146 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 358220004147 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 358220004148 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 358220004149 active site 358220004150 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 358220004151 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220004152 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 358220004153 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220004154 dimerization interface [polypeptide binding]; other site 358220004155 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220004156 dimer interface [polypeptide binding]; other site 358220004157 putative CheW interface [polypeptide binding]; other site 358220004158 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 358220004159 active site 1 [active] 358220004160 dimer interface [polypeptide binding]; other site 358220004161 hexamer interface [polypeptide binding]; other site 358220004162 active site 2 [active] 358220004163 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 358220004164 DHH family; Region: DHH; pfam01368 358220004165 DHHA1 domain; Region: DHHA1; pfam02272 358220004166 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 358220004167 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220004168 AAA domain; Region: AAA_21; pfam13304 358220004169 Walker A/P-loop; other site 358220004170 ATP binding site [chemical binding]; other site 358220004171 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 358220004172 ABC transporter signature motif; other site 358220004173 Walker B; other site 358220004174 D-loop; other site 358220004175 H-loop/switch region; other site 358220004176 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 358220004177 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 358220004178 FtsX-like permease family; Region: FtsX; pfam02687 358220004179 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 358220004180 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 358220004181 Walker A/P-loop; other site 358220004182 ATP binding site [chemical binding]; other site 358220004183 Q-loop/lid; other site 358220004184 ABC transporter signature motif; other site 358220004185 Walker B; other site 358220004186 D-loop; other site 358220004187 H-loop/switch region; other site 358220004188 von Willebrand factor type A domain; Region: VWA_2; pfam13519 358220004189 metal ion-dependent adhesion site (MIDAS); other site 358220004190 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 358220004191 Protein of unknown function DUF58; Region: DUF58; pfam01882 358220004192 MoxR-like ATPases [General function prediction only]; Region: COG0714 358220004193 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220004194 Walker A motif; other site 358220004195 ATP binding site [chemical binding]; other site 358220004196 Walker B motif; other site 358220004197 arginine finger; other site 358220004198 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 358220004199 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 358220004200 active site 358220004201 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 358220004202 putative active site [active] 358220004203 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 358220004204 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 358220004205 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 358220004206 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 358220004207 Walker A motif; other site 358220004208 ATP binding site [chemical binding]; other site 358220004209 Walker B motif; other site 358220004210 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 358220004211 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 358220004212 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 358220004213 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220004214 EamA-like transporter family; Region: EamA; pfam00892 358220004215 EamA-like transporter family; Region: EamA; pfam00892 358220004216 Peptidase family M48; Region: Peptidase_M48; pfam01435 358220004217 Bacterial SH3 domain; Region: SH3_3; cl17532 358220004218 short chain dehydrogenase; Provisional; Region: PRK08339 358220004219 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 358220004220 putative NAD(P) binding site [chemical binding]; other site 358220004221 putative active site [active] 358220004222 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 358220004223 PAS fold; Region: PAS_7; pfam12860 358220004224 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220004225 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220004226 metal binding site [ion binding]; metal-binding site 358220004227 active site 358220004228 I-site; other site 358220004229 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220004230 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220004231 EamA-like transporter family; Region: EamA; pfam00892 358220004232 EamA-like transporter family; Region: EamA; pfam00892 358220004233 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 358220004234 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 358220004235 NADP binding site [chemical binding]; other site 358220004236 dimer interface [polypeptide binding]; other site 358220004237 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 358220004238 nudix motif; other site 358220004239 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 358220004240 atypical (a) SDRs, subgroup 3; Region: SDR_a3; cd05229 358220004241 putative NAD(P) binding site [chemical binding]; other site 358220004242 putative active site [active] 358220004243 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220004244 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220004245 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220004246 putative effector binding pocket; other site 358220004247 dimerization interface [polypeptide binding]; other site 358220004248 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220004249 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220004250 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 358220004251 putative dimerization interface [polypeptide binding]; other site 358220004252 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 358220004253 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 358220004254 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 358220004255 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 358220004256 PhoU domain; Region: PhoU; pfam01895 358220004257 PhoU domain; Region: PhoU; pfam01895 358220004258 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 358220004259 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 358220004260 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 358220004261 active site 358220004262 HIGH motif; other site 358220004263 nucleotide binding site [chemical binding]; other site 358220004264 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 358220004265 active site 358220004266 KMSKS motif; other site 358220004267 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 358220004268 tRNA binding surface [nucleotide binding]; other site 358220004269 anticodon binding site; other site 358220004270 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 358220004271 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 358220004272 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 358220004273 active site 358220004274 Riboflavin kinase; Region: Flavokinase; smart00904 358220004275 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 358220004276 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 358220004277 active site 358220004278 Lipase (class 2); Region: Lipase_2; pfam01674 358220004279 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 358220004280 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 358220004281 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 358220004282 active site 358220004283 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 358220004284 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220004285 active site 358220004286 hypothetical protein; Provisional; Region: PRK11239 358220004287 Protein of unknown function, DUF480; Region: DUF480; pfam04337 358220004288 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 358220004289 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 358220004290 active site 358220004291 substrate binding site [chemical binding]; other site 358220004292 cosubstrate binding site; other site 358220004293 catalytic site [active] 358220004294 Protein of unknown function (DUF1653); Region: DUF1653; pfam07866 358220004295 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 358220004296 ribosomal RNA small subunit methyltransferase RsmB; Region: rsmB; TIGR00563 358220004297 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220004298 S-adenosylmethionine binding site [chemical binding]; other site 358220004299 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 358220004300 Di-iron ligands [ion binding]; other site 358220004301 Transposase; Region: DDE_Tnp_ISL3; pfam01610 358220004302 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 358220004303 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 358220004304 thioredoxin reductase; Provisional; Region: PRK10262 358220004305 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 358220004306 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220004307 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220004308 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220004309 ligand binding site [chemical binding]; other site 358220004310 flexible hinge region; other site 358220004311 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 358220004312 putative switch regulator; other site 358220004313 non-specific DNA interactions [nucleotide binding]; other site 358220004314 DNA binding site [nucleotide binding] 358220004315 sequence specific DNA binding site [nucleotide binding]; other site 358220004316 putative cAMP binding site [chemical binding]; other site 358220004317 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 358220004318 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 358220004319 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 358220004320 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 358220004321 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 358220004322 recombination factor protein RarA; Reviewed; Region: PRK13342 358220004323 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220004324 Walker A motif; other site 358220004325 ATP binding site [chemical binding]; other site 358220004326 Walker B motif; other site 358220004327 arginine finger; other site 358220004328 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 358220004329 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220004330 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220004331 active site 358220004332 phosphorylation site [posttranslational modification] 358220004333 intermolecular recognition site; other site 358220004334 dimerization interface [polypeptide binding]; other site 358220004335 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220004336 DNA binding residues [nucleotide binding] 358220004337 dimerization interface [polypeptide binding]; other site 358220004338 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 358220004339 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220004340 ATP binding site [chemical binding]; other site 358220004341 Mg2+ binding site [ion binding]; other site 358220004342 G-X-G motif; other site 358220004343 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220004344 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220004345 TM-ABC transporter signature motif; other site 358220004346 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220004347 TM-ABC transporter signature motif; other site 358220004348 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220004349 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220004350 Walker A/P-loop; other site 358220004351 ATP binding site [chemical binding]; other site 358220004352 Q-loop/lid; other site 358220004353 ABC transporter signature motif; other site 358220004354 Walker B; other site 358220004355 D-loop; other site 358220004356 H-loop/switch region; other site 358220004357 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220004358 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220004359 Walker A/P-loop; other site 358220004360 ATP binding site [chemical binding]; other site 358220004361 Q-loop/lid; other site 358220004362 ABC transporter signature motif; other site 358220004363 Walker B; other site 358220004364 D-loop; other site 358220004365 H-loop/switch region; other site 358220004366 Protein of unknown function, DUF486; Region: DUF486; pfam04342 358220004367 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 358220004368 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 358220004369 TM2 domain; Region: TM2; pfam05154 358220004370 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 358220004371 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220004372 Coenzyme A binding pocket [chemical binding]; other site 358220004373 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 358220004374 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 358220004375 RimM N-terminal domain; Region: RimM; pfam01782 358220004376 PRC-barrel domain; Region: PRC; pfam05239 358220004377 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 358220004378 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 358220004379 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 358220004380 putative active site [active] 358220004381 putative CoA binding site [chemical binding]; other site 358220004382 nudix motif; other site 358220004383 metal binding site [ion binding]; metal-binding site 358220004384 CobD/Cbib protein; Region: CobD_Cbib; cl00561 358220004385 GTPase RsgA; Reviewed; Region: PRK00098 358220004386 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 358220004387 RNA binding site [nucleotide binding]; other site 358220004388 homodimer interface [polypeptide binding]; other site 358220004389 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 358220004390 GTPase/Zn-binding domain interface [polypeptide binding]; other site 358220004391 GTP/Mg2+ binding site [chemical binding]; other site 358220004392 G4 box; other site 358220004393 G5 box; other site 358220004394 G1 box; other site 358220004395 Switch I region; other site 358220004396 G2 box; other site 358220004397 G3 box; other site 358220004398 Switch II region; other site 358220004399 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cd00488 358220004400 aromatic arch; other site 358220004401 DCoH dimer interaction site [polypeptide binding]; other site 358220004402 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 358220004403 DCoH tetramer interaction site [polypeptide binding]; other site 358220004404 substrate binding site [chemical binding]; other site 358220004405 Peptidase family M48; Region: Peptidase_M48; pfam01435 358220004406 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 358220004407 catalytic site [active] 358220004408 putative active site [active] 358220004409 putative substrate binding site [chemical binding]; other site 358220004410 dimer interface [polypeptide binding]; other site 358220004411 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 358220004412 DEAD-like helicases superfamily; Region: DEXDc; smart00487 358220004413 ATP binding site [chemical binding]; other site 358220004414 Mg++ binding site [ion binding]; other site 358220004415 motif III; other site 358220004416 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220004417 nucleotide binding region [chemical binding]; other site 358220004418 ATP-binding site [chemical binding]; other site 358220004419 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 358220004420 PAS domain; Region: PAS_9; pfam13426 358220004421 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220004422 PAS domain; Region: PAS_9; pfam13426 358220004423 putative active site [active] 358220004424 heme pocket [chemical binding]; other site 358220004425 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220004426 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220004427 metal binding site [ion binding]; metal-binding site 358220004428 active site 358220004429 I-site; other site 358220004430 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220004431 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 358220004432 putative substrate translocation pore; other site 358220004433 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 358220004434 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 358220004435 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 358220004436 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220004437 substrate binding pocket [chemical binding]; other site 358220004438 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 358220004439 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 358220004440 active site 358220004441 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 358220004442 Part of AAA domain; Region: AAA_19; pfam13245 358220004443 Family description; Region: UvrD_C_2; pfam13538 358220004444 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 358220004445 FecR protein; Region: FecR; pfam04773 358220004446 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 358220004447 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 358220004448 putative active site [active] 358220004449 putative substrate binding site [chemical binding]; other site 358220004450 ATP binding site [chemical binding]; other site 358220004451 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 358220004452 DNA polymerase I; Provisional; Region: PRK05755 358220004453 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 358220004454 active site 358220004455 metal binding site 1 [ion binding]; metal-binding site 358220004456 putative 5' ssDNA interaction site; other site 358220004457 metal binding site 3; metal-binding site 358220004458 metal binding site 2 [ion binding]; metal-binding site 358220004459 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 358220004460 putative DNA binding site [nucleotide binding]; other site 358220004461 putative metal binding site [ion binding]; other site 358220004462 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 358220004463 active site 358220004464 catalytic site [active] 358220004465 substrate binding site [chemical binding]; other site 358220004466 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 358220004467 active site 358220004468 DNA binding site [nucleotide binding] 358220004469 catalytic site [active] 358220004470 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 358220004471 Pretoxin HINT domain; Region: PT-HINT; pfam07591 358220004472 thioester formation/cholesterol transfer; other site 358220004473 protein-splicing catalytic site; other site 358220004474 putative S-transferase; Provisional; Region: PRK11752 358220004475 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 358220004476 C-terminal domain interface [polypeptide binding]; other site 358220004477 GSH binding site (G-site) [chemical binding]; other site 358220004478 dimer interface [polypeptide binding]; other site 358220004479 C-terminal, alpha helical domain of Escherichia coli Yghu Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YghU_like; cd10292 358220004480 dimer interface [polypeptide binding]; other site 358220004481 N-terminal domain interface [polypeptide binding]; other site 358220004482 active site 358220004483 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220004484 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 358220004485 putative C-terminal domain interface [polypeptide binding]; other site 358220004486 putative GSH binding site (G-site) [chemical binding]; other site 358220004487 putative dimer interface [polypeptide binding]; other site 358220004488 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 358220004489 N-terminal domain interface [polypeptide binding]; other site 358220004490 dimer interface [polypeptide binding]; other site 358220004491 substrate binding pocket (H-site) [chemical binding]; other site 358220004492 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 358220004493 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220004494 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220004495 dimerization interface [polypeptide binding]; other site 358220004496 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 358220004497 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 358220004498 hydroxyglutarate oxidase; Provisional; Region: PRK11728 358220004499 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220004500 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220004501 substrate binding pocket [chemical binding]; other site 358220004502 membrane-bound complex binding site; other site 358220004503 hinge residues; other site 358220004504 aspartate racemase; Region: asp_race; TIGR00035 358220004505 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 358220004506 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220004507 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220004508 substrate binding pocket [chemical binding]; other site 358220004509 membrane-bound complex binding site; other site 358220004510 hinge residues; other site 358220004511 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 358220004512 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 358220004513 putative NAD(P) binding site [chemical binding]; other site 358220004514 active site 358220004515 PAS fold; Region: PAS_7; pfam12860 358220004516 PAS fold; Region: PAS_7; pfam12860 358220004517 PAS fold; Region: PAS_7; pfam12860 358220004518 PAS fold; Region: PAS_7; pfam12860 358220004519 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220004520 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220004521 metal binding site [ion binding]; metal-binding site 358220004522 active site 358220004523 I-site; other site 358220004524 Dienelactone hydrolase family; Region: DLH; pfam01738 358220004525 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 358220004526 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 358220004527 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 358220004528 P loop; other site 358220004529 Nucleotide binding site [chemical binding]; other site 358220004530 DTAP/Switch II; other site 358220004531 Switch I; other site 358220004532 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 358220004533 P loop; other site 358220004534 Nucleotide binding site [chemical binding]; other site 358220004535 DTAP/Switch II; other site 358220004536 Switch I; other site 358220004537 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 358220004538 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220004539 active site 358220004540 phosphorylation site [posttranslational modification] 358220004541 intermolecular recognition site; other site 358220004542 dimerization interface [polypeptide binding]; other site 358220004543 LytTr DNA-binding domain; Region: LytTR; smart00850 358220004544 Histidine kinase; Region: His_kinase; pfam06580 358220004545 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 358220004546 Mg2+ binding site [ion binding]; other site 358220004547 argininosuccinate lyase; Provisional; Region: PRK00855 358220004548 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 358220004549 active sites [active] 358220004550 tetramer interface [polypeptide binding]; other site 358220004551 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220004552 CHASE domain; Region: CHASE; cl01369 358220004553 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220004554 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220004555 metal binding site [ion binding]; metal-binding site 358220004556 active site 358220004557 I-site; other site 358220004558 hydroperoxidase II; Provisional; Region: katE; PRK11249 358220004559 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 358220004560 tetramer interface [polypeptide binding]; other site 358220004561 heme binding pocket [chemical binding]; other site 358220004562 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 358220004563 domain interactions; other site 358220004564 Bacterial Ig-like domain; Region: Big_5; pfam13205 358220004565 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 358220004566 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 358220004567 MG2 domain; Region: A2M_N; pfam01835 358220004568 Alpha-2-macroglobulin family; Region: A2M; pfam00207 358220004569 MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate...; Region: MGS-like; cl00245 358220004570 substrate binding site [chemical binding]; other site 358220004571 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 358220004572 Transglycosylase; Region: Transgly; pfam00912 358220004573 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 358220004574 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 358220004575 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220004576 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220004577 putative active site [active] 358220004578 heme pocket [chemical binding]; other site 358220004579 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220004580 putative active site [active] 358220004581 heme pocket [chemical binding]; other site 358220004582 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220004583 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220004584 metal binding site [ion binding]; metal-binding site 358220004585 active site 358220004586 I-site; other site 358220004587 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 358220004588 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 358220004589 phosphate binding site [ion binding]; other site 358220004590 Cytochrome c; Region: Cytochrom_C; cl11414 358220004591 RNA polymerase sigma factor; Provisional; Region: PRK12514 358220004592 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220004593 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220004594 DNA binding residues [nucleotide binding] 358220004595 Anti-sigma-K factor rskA; Region: RskA; pfam10099 358220004596 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 358220004597 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 358220004598 apolar tunnel; other site 358220004599 heme binding site [chemical binding]; other site 358220004600 dimerization interface [polypeptide binding]; other site 358220004601 Cytochrome c; Region: Cytochrom_C; pfam00034 358220004602 Domain of unknown function (DUF4336); Region: DUF4336; pfam14234 358220004603 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 358220004604 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 358220004605 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220004606 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220004607 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 358220004608 dimerization interface [polypeptide binding]; other site 358220004609 substrate binding pocket [chemical binding]; other site 358220004610 aldehyde dehydrogenase family 7 member; Region: PLN02315 358220004611 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 358220004612 tetrameric interface [polypeptide binding]; other site 358220004613 NAD binding site [chemical binding]; other site 358220004614 catalytic residues [active] 358220004615 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 358220004616 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220004617 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220004618 substrate binding pocket [chemical binding]; other site 358220004619 membrane-bound complex binding site; other site 358220004620 hinge residues; other site 358220004621 aspartate aminotransferase; Provisional; Region: PRK05764 358220004622 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220004623 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220004624 homodimer interface [polypeptide binding]; other site 358220004625 catalytic residue [active] 358220004626 thiamine pyrophosphate protein; Validated; Region: PRK08199 358220004627 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 358220004628 PYR/PP interface [polypeptide binding]; other site 358220004629 dimer interface [polypeptide binding]; other site 358220004630 TPP binding site [chemical binding]; other site 358220004631 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 358220004632 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 358220004633 TPP-binding site [chemical binding]; other site 358220004634 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220004635 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220004636 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220004637 dimerization interface [polypeptide binding]; other site 358220004638 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220004639 EamA-like transporter family; Region: EamA; pfam00892 358220004640 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 358220004641 active site 358220004642 DNA polymerase IV; Validated; Region: PRK02406 358220004643 DNA binding site [nucleotide binding] 358220004644 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220004645 PAS domain; Region: PAS_9; pfam13426 358220004646 putative active site [active] 358220004647 heme pocket [chemical binding]; other site 358220004648 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220004649 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220004650 dimer interface [polypeptide binding]; other site 358220004651 putative CheW interface [polypeptide binding]; other site 358220004652 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 358220004653 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 358220004654 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 358220004655 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 358220004656 hypothetical protein; Validated; Region: PRK02101 358220004657 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 358220004658 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 358220004659 homodimer interface [polypeptide binding]; other site 358220004660 oligonucleotide binding site [chemical binding]; other site 358220004661 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 358220004662 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 358220004663 RNA binding surface [nucleotide binding]; other site 358220004664 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 358220004665 active site 358220004666 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 358220004667 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220004668 motif II; other site 358220004669 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 358220004670 iron-sulfur cluster [ion binding]; other site 358220004671 [2Fe-2S] cluster binding site [ion binding]; other site 358220004672 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 358220004673 tandem repeat interface [polypeptide binding]; other site 358220004674 oligomer interface [polypeptide binding]; other site 358220004675 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 358220004676 active site residues [active] 358220004677 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 358220004678 putative SAM binding site [chemical binding]; other site 358220004679 homodimer interface [polypeptide binding]; other site 358220004680 Maf-like protein; Region: Maf; pfam02545 358220004681 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 358220004682 active site 358220004683 dimer interface [polypeptide binding]; other site 358220004684 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 358220004685 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 358220004686 putative phosphate acyltransferase; Provisional; Region: PRK05331 358220004687 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 358220004688 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 358220004689 dimer interface [polypeptide binding]; other site 358220004690 active site 358220004691 CoA binding pocket [chemical binding]; other site 358220004692 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 358220004693 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 358220004694 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 358220004695 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 358220004696 NAD(P) binding site [chemical binding]; other site 358220004697 homotetramer interface [polypeptide binding]; other site 358220004698 homodimer interface [polypeptide binding]; other site 358220004699 active site 358220004700 acyl carrier protein; Provisional; Region: acpP; PRK00982 358220004701 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 358220004702 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 358220004703 dimer interface [polypeptide binding]; other site 358220004704 active site 358220004705 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 358220004706 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220004707 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220004708 DNA binding residues [nucleotide binding] 358220004709 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 358220004710 MucB/RseB family; Region: MucB_RseB; pfam03888 358220004711 anti-sigma E factor; Provisional; Region: rseB; PRK09455 358220004712 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 358220004713 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 358220004714 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 358220004715 protein binding site [polypeptide binding]; other site 358220004716 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 358220004717 GTP-binding protein LepA; Provisional; Region: PRK05433 358220004718 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 358220004719 G1 box; other site 358220004720 putative GEF interaction site [polypeptide binding]; other site 358220004721 GTP/Mg2+ binding site [chemical binding]; other site 358220004722 Switch I region; other site 358220004723 G2 box; other site 358220004724 G3 box; other site 358220004725 Switch II region; other site 358220004726 G4 box; other site 358220004727 G5 box; other site 358220004728 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 358220004729 lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits...; Region: lepA_C; cd03709 358220004730 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 358220004731 signal peptidase I; Provisional; Region: PRK10861 358220004732 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 358220004733 Catalytic site [active] 358220004734 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 358220004735 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 358220004736 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 358220004737 dimerization interface [polypeptide binding]; other site 358220004738 active site 358220004739 metal binding site [ion binding]; metal-binding site 358220004740 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 358220004741 dsRNA binding site [nucleotide binding]; other site 358220004742 GTPase Era; Reviewed; Region: era; PRK00089 358220004743 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 358220004744 G1 box; other site 358220004745 GTP/Mg2+ binding site [chemical binding]; other site 358220004746 Switch I region; other site 358220004747 G2 box; other site 358220004748 Switch II region; other site 358220004749 G3 box; other site 358220004750 G4 box; other site 358220004751 G5 box; other site 358220004752 KH domain; Region: KH_2; pfam07650 358220004753 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 358220004754 Recombination protein O N terminal; Region: RecO_N; pfam11967 358220004755 Recombination protein O C terminal; Region: RecO_C; pfam02565 358220004756 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 358220004757 active site 358220004758 hydrophilic channel; other site 358220004759 dimerization interface [polypeptide binding]; other site 358220004760 catalytic residues [active] 358220004761 active site lid [active] 358220004762 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 358220004763 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 358220004764 beta-hexosaminidase; Provisional; Region: PRK05337 358220004765 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 358220004766 Mechanosensitive ion channel; Region: MS_channel; pfam00924 358220004767 Response regulator receiver domain; Region: Response_reg; pfam00072 358220004768 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220004769 active site 358220004770 phosphorylation site [posttranslational modification] 358220004771 intermolecular recognition site; other site 358220004772 dimerization interface [polypeptide binding]; other site 358220004773 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220004774 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220004775 metal binding site [ion binding]; metal-binding site 358220004776 active site 358220004777 I-site; other site 358220004778 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 358220004779 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 358220004780 dimer interface [polypeptide binding]; other site 358220004781 putative anticodon binding site; other site 358220004782 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 358220004783 motif 1; other site 358220004784 active site 358220004785 motif 2; other site 358220004786 motif 3; other site 358220004787 Bacterial sugar transferase; Region: Bac_transf; pfam02397 358220004788 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 358220004789 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 358220004790 inhibitor-cofactor binding pocket; inhibition site 358220004791 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220004792 catalytic residue [active] 358220004793 Methyltransferase domain; Region: Methyltransf_11; pfam08241 358220004794 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 358220004795 putative glycosyl transferase; Provisional; Region: PRK10307 358220004796 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 358220004797 active site 358220004798 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 358220004799 homodimer interface [polypeptide binding]; other site 358220004800 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220004801 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 358220004802 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220004803 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 358220004804 Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]; Region: AsnB; COG0367 358220004805 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 358220004806 active site 358220004807 dimer interface [polypeptide binding]; other site 358220004808 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 358220004809 Ligand Binding Site [chemical binding]; other site 358220004810 Molecular Tunnel; other site 358220004811 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 358220004812 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220004813 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 358220004814 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 358220004815 potential frameshift: common BLAST hit: gi|387829229|ref|YP_003349166.1| transposase 358220004816 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220004817 Transposase; Region: HTH_Tnp_1; pfam01527 358220004818 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 358220004819 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 358220004820 inhibitor-cofactor binding pocket; inhibition site 358220004821 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220004822 catalytic residue [active] 358220004823 Bacterial transferase hexapeptide (six repeats); Region: Hexapep; pfam00132 358220004824 putative CoA binding site [chemical binding]; other site 358220004825 putative trimer interface [polypeptide binding]; other site 358220004826 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 358220004827 putative trimer interface [polypeptide binding]; other site 358220004828 putative active site [active] 358220004829 putative substrate binding site [chemical binding]; other site 358220004830 putative CoA binding site [chemical binding]; other site 358220004831 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 358220004832 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 358220004833 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 358220004834 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 358220004835 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 358220004836 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 358220004837 Integrase core domain; Region: rve; pfam00665 358220004838 Integrase core domain; Region: rve_3; pfam13683 358220004839 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 358220004840 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 358220004841 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 358220004842 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 358220004843 NAD(P) binding site [chemical binding]; other site 358220004844 homodimer interface [polypeptide binding]; other site 358220004845 substrate binding site [chemical binding]; other site 358220004846 active site 358220004847 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 358220004848 YGGT family; Region: YGGT; pfam02325 358220004849 YGGT family; Region: YGGT; pfam02325 358220004850 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 358220004851 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 358220004852 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 358220004853 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 358220004854 substrate binding site [chemical binding]; other site 358220004855 active site 358220004856 catalytic residues [active] 358220004857 heterodimer interface [polypeptide binding]; other site 358220004858 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 358220004859 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 358220004860 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220004861 catalytic residue [active] 358220004862 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 358220004863 active site 358220004864 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 358220004865 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 358220004866 dimerization interface 3.5A [polypeptide binding]; other site 358220004867 active site 358220004868 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 358220004869 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 358220004870 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 358220004871 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 358220004872 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 358220004873 tartrate dehydrogenase; Region: TTC; TIGR02089 358220004874 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 358220004875 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 358220004876 substrate binding site [chemical binding]; other site 358220004877 Entericidin EcnA/B family; Region: Entericidin; cl02322 358220004878 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 358220004879 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 358220004880 substrate binding site [chemical binding]; other site 358220004881 ligand binding site [chemical binding]; other site 358220004882 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220004883 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220004884 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 358220004885 putative dimerization interface [polypeptide binding]; other site 358220004886 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 358220004887 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 358220004888 Beta-Casp domain; Region: Beta-Casp; pfam10996 358220004889 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 358220004890 chaperone protein DnaJ; Provisional; Region: PRK10767 358220004891 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 358220004892 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 358220004893 substrate binding site [polypeptide binding]; other site 358220004894 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 358220004895 Zn binding sites [ion binding]; other site 358220004896 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 358220004897 dimer interface [polypeptide binding]; other site 358220004898 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 358220004899 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 358220004900 nucleotide binding site [chemical binding]; other site 358220004901 GrpE; Region: GrpE; pfam01025 358220004902 GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding; Region: GrpE; cd00446 358220004903 dimer interface [polypeptide binding]; other site 358220004904 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 358220004905 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 358220004906 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 358220004907 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 358220004908 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 358220004909 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 358220004910 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 358220004911 replicative DNA helicase; Region: DnaB; TIGR00665 358220004912 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 358220004913 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 358220004914 Walker A motif; other site 358220004915 ATP binding site [chemical binding]; other site 358220004916 Walker B motif; other site 358220004917 DNA binding loops [nucleotide binding] 358220004918 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 358220004919 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 358220004920 putative active site [active] 358220004921 PhoH-like protein; Region: PhoH; pfam02562 358220004922 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 358220004923 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 358220004924 catalytic triad [active] 358220004925 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 358220004926 aminotransferase AlaT; Validated; Region: PRK09265 358220004927 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220004928 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220004929 homodimer interface [polypeptide binding]; other site 358220004930 catalytic residue [active] 358220004931 Protein of unknown function (DUF1176); Region: DUF1176; pfam06674 358220004932 homoserine dehydrogenase; Provisional; Region: PRK06349 358220004933 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 358220004934 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 358220004935 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 358220004936 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 358220004937 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 358220004938 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220004939 catalytic residue [active] 358220004940 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 358220004941 Walker A motif; other site 358220004942 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 358220004943 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 358220004944 dimer interface [polypeptide binding]; other site 358220004945 putative functional site; other site 358220004946 putative MPT binding site; other site 358220004947 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 358220004948 MoaE interaction surface [polypeptide binding]; other site 358220004949 MoeB interaction surface [polypeptide binding]; other site 358220004950 thiocarboxylated glycine; other site 358220004951 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 358220004952 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 358220004953 dimer interface [polypeptide binding]; other site 358220004954 active site 358220004955 catalytic residue [active] 358220004956 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 358220004957 MoaE homodimer interface [polypeptide binding]; other site 358220004958 MoaD interaction [polypeptide binding]; other site 358220004959 active site residues [active] 358220004960 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 358220004961 16S/18S rRNA binding site [nucleotide binding]; other site 358220004962 S13e-L30e interaction site [polypeptide binding]; other site 358220004963 25S rRNA binding site [nucleotide binding]; other site 358220004964 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 358220004965 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 358220004966 RNase E interface [polypeptide binding]; other site 358220004967 trimer interface [polypeptide binding]; other site 358220004968 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 358220004969 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 358220004970 RNase E interface [polypeptide binding]; other site 358220004971 trimer interface [polypeptide binding]; other site 358220004972 active site 358220004973 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 358220004974 putative nucleic acid binding region [nucleotide binding]; other site 358220004975 G-X-X-G motif; other site 358220004976 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 358220004977 RNA binding site [nucleotide binding]; other site 358220004978 domain interface; other site 358220004979 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 358220004980 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 358220004981 NAD(P) binding site [chemical binding]; other site 358220004982 triosephosphate isomerase; Provisional; Region: PRK14567 358220004983 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 358220004984 substrate binding site [chemical binding]; other site 358220004985 dimer interface [polypeptide binding]; other site 358220004986 catalytic triad [active] 358220004987 Preprotein translocase SecG subunit; Region: SecG; pfam03840 358220004988 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 358220004989 NADH dehydrogenase subunit B; Validated; Region: PRK06411 358220004990 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 358220004991 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 358220004992 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 358220004993 NADH dehydrogenase subunit D; Validated; Region: PRK06075 358220004994 NADH dehydrogenase subunit E; Validated; Region: PRK07539 358220004995 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 358220004996 putative dimer interface [polypeptide binding]; other site 358220004997 [2Fe-2S] cluster binding site [ion binding]; other site 358220004998 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 358220004999 SLBB domain; Region: SLBB; pfam10531 358220005000 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 358220005001 NADH dehydrogenase subunit G; Validated; Region: PRK09129 358220005002 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220005003 catalytic loop [active] 358220005004 iron binding site [ion binding]; other site 358220005005 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 358220005006 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 358220005007 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 358220005008 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 358220005009 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 358220005010 4Fe-4S binding domain; Region: Fer4; pfam00037 358220005011 4Fe-4S binding domain; Region: Fer4; pfam00037 358220005012 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 358220005013 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 358220005014 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 358220005015 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 358220005016 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 358220005017 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 358220005018 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 358220005019 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 358220005020 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 358220005021 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 358220005022 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 358220005023 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 358220005024 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 358220005025 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 358220005026 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 358220005027 Walker A/P-loop; other site 358220005028 ATP binding site [chemical binding]; other site 358220005029 Q-loop/lid; other site 358220005030 ABC transporter signature motif; other site 358220005031 Walker B; other site 358220005032 D-loop; other site 358220005033 H-loop/switch region; other site 358220005034 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220005035 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220005036 Walker A/P-loop; other site 358220005037 ATP binding site [chemical binding]; other site 358220005038 Q-loop/lid; other site 358220005039 ABC transporter signature motif; other site 358220005040 Walker B; other site 358220005041 D-loop; other site 358220005042 H-loop/switch region; other site 358220005043 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220005044 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220005045 Walker A/P-loop; other site 358220005046 ATP binding site [chemical binding]; other site 358220005047 Q-loop/lid; other site 358220005048 ABC transporter signature motif; other site 358220005049 Walker B; other site 358220005050 D-loop; other site 358220005051 H-loop/switch region; other site 358220005052 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220005053 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 358220005054 putative ligand binding site [chemical binding]; other site 358220005055 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220005056 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220005057 TM-ABC transporter signature motif; other site 358220005058 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220005059 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220005060 TM-ABC transporter signature motif; other site 358220005061 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 358220005062 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 358220005063 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 358220005064 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220005065 catalytic residue [active] 358220005066 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220005067 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220005068 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220005069 dimerization interface [polypeptide binding]; other site 358220005070 Protein of unknown function (DUF4242); Region: DUF4242; pfam14026 358220005071 FtsX-like permease family; Region: FtsX; pfam02687 358220005072 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 358220005073 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 358220005074 putative dimer interface [polypeptide binding]; other site 358220005075 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 358220005076 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 358220005077 Walker A/P-loop; other site 358220005078 ATP binding site [chemical binding]; other site 358220005079 Q-loop/lid; other site 358220005080 ABC transporter signature motif; other site 358220005081 Walker B; other site 358220005082 D-loop; other site 358220005083 H-loop/switch region; other site 358220005084 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 358220005085 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 358220005086 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 358220005087 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220005088 putative substrate translocation pore; other site 358220005089 Beta-lactamase; Region: Beta-lactamase; pfam00144 358220005090 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 358220005091 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 358220005092 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 358220005093 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 358220005094 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 358220005095 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220005096 Walker A motif; other site 358220005097 ATP binding site [chemical binding]; other site 358220005098 Walker B motif; other site 358220005099 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 358220005100 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220005101 Walker A motif; other site 358220005102 ATP binding site [chemical binding]; other site 358220005103 Walker B motif; other site 358220005104 glutamate dehydrogenase; Provisional; Region: PRK09414 358220005105 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 358220005106 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 358220005107 NAD(P) binding site [chemical binding]; other site 358220005108 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 358220005109 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 358220005110 putative active site [active] 358220005111 catalytic site [active] 358220005112 putative metal binding site [ion binding]; other site 358220005113 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 358220005114 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220005115 ATP binding site [chemical binding]; other site 358220005116 Mg2+ binding site [ion binding]; other site 358220005117 G-X-G motif; other site 358220005118 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 358220005119 ATP binding site [chemical binding]; other site 358220005120 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 358220005121 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 358220005122 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 358220005123 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220005124 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220005125 dimerization interface [polypeptide binding]; other site 358220005126 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220005127 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220005128 dimer interface [polypeptide binding]; other site 358220005129 putative CheW interface [polypeptide binding]; other site 358220005130 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 358220005131 AMIN domain; Region: AMIN; pfam11741 358220005132 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 358220005133 active site 358220005134 metal binding site [ion binding]; metal-binding site 358220005135 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 358220005136 epoxyqueuosine reductase; Region: TIGR00276 358220005137 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 358220005138 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 358220005139 active site 358220005140 catalytic triad [active] 358220005141 oxyanion hole [active] 358220005142 switch loop; other site 358220005143 Predicted permeases [General function prediction only]; Region: COG0679 358220005144 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220005145 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 358220005146 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 358220005147 active site 358220005148 Int/Topo IB signature motif; other site 358220005149 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220005150 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220005151 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 358220005152 EAL domain; Region: EAL; pfam00563 358220005153 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 358220005154 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 358220005155 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 358220005156 dinuclear metal binding motif [ion binding]; other site 358220005157 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 358220005158 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 358220005159 trimer interface [polypeptide binding]; other site 358220005160 putative metal binding site [ion binding]; other site 358220005161 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 358220005162 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 358220005163 dimerization interface [polypeptide binding]; other site 358220005164 domain crossover interface; other site 358220005165 redox-dependent activation switch; other site 358220005166 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 358220005167 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 358220005168 Septum formation initiator; Region: DivIC; cl17659 358220005169 enolase; Provisional; Region: eno; PRK00077 358220005170 Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions; Region: enolase; cd03313 358220005171 dimer interface [polypeptide binding]; other site 358220005172 metal binding site [ion binding]; metal-binding site 358220005173 substrate binding pocket [chemical binding]; other site 358220005174 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 358220005175 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 358220005176 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 358220005177 CTP synthetase; Validated; Region: pyrG; PRK05380 358220005178 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 358220005179 Catalytic site [active] 358220005180 active site 358220005181 UTP binding site [chemical binding]; other site 358220005182 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 358220005183 active site 358220005184 putative oxyanion hole; other site 358220005185 catalytic triad [active] 358220005186 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 358220005187 Flavoprotein; Region: Flavoprotein; pfam02441 358220005188 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 358220005189 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 358220005190 trimer interface [polypeptide binding]; other site 358220005191 active site 358220005192 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 358220005193 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 358220005194 Uncharacterized conserved protein [Function unknown]; Region: COG2850 358220005195 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 358220005196 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 358220005197 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 358220005198 dihydrodipicolinate synthase; Region: dapA; TIGR00674 358220005199 dimer interface [polypeptide binding]; other site 358220005200 active site 358220005201 catalytic residue [active] 358220005202 Methyltransferase domain; Region: Methyltransf_23; pfam13489 358220005203 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220005204 S-adenosylmethionine binding site [chemical binding]; other site 358220005205 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220005206 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220005207 putative substrate translocation pore; other site 358220005208 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 358220005209 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220005210 ATP binding site [chemical binding]; other site 358220005211 Mg2+ binding site [ion binding]; other site 358220005212 G-X-G motif; other site 358220005213 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 358220005214 anchoring element; other site 358220005215 dimer interface [polypeptide binding]; other site 358220005216 ATP binding site [chemical binding]; other site 358220005217 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 358220005218 active site 358220005219 metal binding site [ion binding]; metal-binding site 358220005220 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 358220005221 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 358220005222 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 358220005223 N-acetyl-D-glucosamine binding site [chemical binding]; other site 358220005224 catalytic residue [active] 358220005225 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 358220005226 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 358220005227 CAP-like domain; other site 358220005228 active site 358220005229 primary dimer interface [polypeptide binding]; other site 358220005230 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 358220005231 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220005232 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220005233 dimerization interface [polypeptide binding]; other site 358220005234 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220005235 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220005236 dimer interface [polypeptide binding]; other site 358220005237 putative CheW interface [polypeptide binding]; other site 358220005238 putative transposase OrfB; Reviewed; Region: PHA02517 358220005239 Integrase core domain; Region: rve; pfam00665 358220005240 Integrase core domain; Region: rve_3; pfam13683 358220005241 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220005242 Homeodomain-like domain; Region: HTH_23; cl17451 358220005243 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 358220005244 homotrimer interaction site [polypeptide binding]; other site 358220005245 putative active site [active] 358220005246 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 358220005247 Competence protein; Region: Competence; pfam03772 358220005248 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 358220005249 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 358220005250 Uncharacterized conserved protein [Function unknown]; Region: COG2308 358220005251 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 358220005252 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 358220005253 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 358220005254 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 358220005255 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220005256 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220005257 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 358220005258 putative effector binding pocket; other site 358220005259 putative dimerization interface [polypeptide binding]; other site 358220005260 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 358220005261 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 358220005262 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220005263 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220005264 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 358220005265 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 358220005266 aspartate aminotransferase; Provisional; Region: PRK06108 358220005267 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220005268 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220005269 homodimer interface [polypeptide binding]; other site 358220005270 catalytic residue [active] 358220005271 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 358220005272 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 358220005273 tetramerization interface [polypeptide binding]; other site 358220005274 NAD(P) binding site [chemical binding]; other site 358220005275 catalytic residues [active] 358220005276 Uncharacterized conserved protein [Function unknown]; Region: COG1262 358220005277 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 358220005278 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 358220005279 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 358220005280 trimer interface [polypeptide binding]; other site 358220005281 eyelet of channel; other site 358220005282 potential frameshift: common BLAST hit: gi|333915274|ref|YP_004489006.1| TonB-dependent siderophore receptor 358220005283 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 358220005284 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 358220005285 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 358220005286 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 358220005287 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 358220005288 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 358220005289 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 358220005290 N-terminal plug; other site 358220005291 ligand-binding site [chemical binding]; other site 358220005292 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 358220005293 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 358220005294 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 358220005295 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 358220005296 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 358220005297 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 358220005298 heme binding site [chemical binding]; other site 358220005299 ferroxidase pore; other site 358220005300 ferroxidase diiron center [ion binding]; other site 358220005301 peroxiredoxin; Region: AhpC; TIGR03137 358220005302 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 358220005303 dimer interface [polypeptide binding]; other site 358220005304 decamer (pentamer of dimers) interface [polypeptide binding]; other site 358220005305 catalytic triad [active] 358220005306 peroxidatic and resolving cysteines [active] 358220005307 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 358220005308 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 358220005309 catalytic residue [active] 358220005310 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 358220005311 catalytic residues [active] 358220005312 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 358220005313 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220005314 PEP synthetase regulatory protein; Provisional; Region: PRK05339 358220005315 phosphoenolpyruvate synthase; Validated; Region: PRK06464 358220005316 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 358220005317 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 358220005318 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 358220005319 Domain of unknown function (DUF4212); Region: DUF4212; cl01781 358220005320 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 358220005321 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 358220005322 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 358220005323 Predicted transcriptional regulators [Transcription]; Region: COG1733 358220005324 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 358220005325 dimerization interface [polypeptide binding]; other site 358220005326 putative DNA binding site [nucleotide binding]; other site 358220005327 putative Zn2+ binding site [ion binding]; other site 358220005328 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220005329 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220005330 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 358220005331 putative dimerization interface [polypeptide binding]; other site 358220005332 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 358220005333 active site 358220005334 catalytic residues [active] 358220005335 metal binding site [ion binding]; metal-binding site 358220005336 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 358220005337 CoA-transferase family III; Region: CoA_transf_3; pfam02515 358220005338 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220005339 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220005340 dimerization interface [polypeptide binding]; other site 358220005341 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220005342 dimer interface [polypeptide binding]; other site 358220005343 putative CheW interface [polypeptide binding]; other site 358220005344 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220005345 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 358220005346 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 358220005347 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 358220005348 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 358220005349 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220005350 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 358220005351 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220005352 DNA binding residues [nucleotide binding] 358220005353 DNA primase, catalytic core; Region: dnaG; TIGR01391 358220005354 CHC2 zinc finger; Region: zf-CHC2; pfam01807 358220005355 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 358220005356 TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_DnaG_primases; cd03364 358220005357 active site 358220005358 metal binding site [ion binding]; metal-binding site 358220005359 interdomain interaction site; other site 358220005360 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 358220005361 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 358220005362 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 358220005363 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 358220005364 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220005365 dimerization interface [polypeptide binding]; other site 358220005366 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220005367 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220005368 metal binding site [ion binding]; metal-binding site 358220005369 active site 358220005370 I-site; other site 358220005371 acyl-CoA synthetase; Validated; Region: PRK08162 358220005372 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 358220005373 acyl-activating enzyme (AAE) consensus motif; other site 358220005374 putative active site [active] 358220005375 AMP binding site [chemical binding]; other site 358220005376 putative CoA binding site [chemical binding]; other site 358220005377 Cupin; Region: Cupin_6; pfam12852 358220005378 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220005379 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 358220005380 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220005381 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 358220005382 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 358220005383 PPOX class probable FMN-dependent enzyme, DR_2398 family; Region: PPOX_FMN_DR2398; TIGR04025 358220005384 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 358220005385 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220005386 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220005387 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 358220005388 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 358220005389 NADP binding site [chemical binding]; other site 358220005390 dimer interface [polypeptide binding]; other site 358220005391 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220005392 CoenzymeA binding site [chemical binding]; other site 358220005393 subunit interaction site [polypeptide binding]; other site 358220005394 PHB binding site; other site 358220005395 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 358220005396 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 358220005397 PhoD-like phosphatase; Region: PhoD; pfam09423 358220005398 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 358220005399 putative active site [active] 358220005400 putative metal binding site [ion binding]; other site 358220005401 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 358220005402 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220005403 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220005404 metal binding site [ion binding]; metal-binding site 358220005405 active site 358220005406 I-site; other site 358220005407 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 358220005408 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 358220005409 NAD(P) binding site [chemical binding]; other site 358220005410 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 358220005411 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 358220005412 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220005413 S-adenosylmethionine binding site [chemical binding]; other site 358220005414 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 358220005415 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 358220005416 Peptidase family M23; Region: Peptidase_M23; pfam01551 358220005417 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 358220005418 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 358220005419 RNA binding surface [nucleotide binding]; other site 358220005420 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 358220005421 active site 358220005422 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 358220005423 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 358220005424 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 358220005425 RNA binding surface [nucleotide binding]; other site 358220005426 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 358220005427 probable active site [active] 358220005428 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 358220005429 active site 358220005430 multimer interface [polypeptide binding]; other site 358220005431 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 358220005432 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 358220005433 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 358220005434 binding surface 358220005435 TPR motif; other site 358220005436 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 358220005437 binding surface 358220005438 TPR motif; other site 358220005439 Helix-turn-helix domain; Region: HTH_25; pfam13413 358220005440 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 358220005441 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 358220005442 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 358220005443 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 358220005444 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 358220005445 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 358220005446 dimer interface [polypeptide binding]; other site 358220005447 motif 1; other site 358220005448 active site 358220005449 motif 2; other site 358220005450 motif 3; other site 358220005451 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 358220005452 anticodon binding site; other site 358220005453 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 358220005454 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 358220005455 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 358220005456 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 358220005457 Trp docking motif [polypeptide binding]; other site 358220005458 active site 358220005459 GTP-binding protein Der; Reviewed; Region: PRK00093 358220005460 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 358220005461 G1 box; other site 358220005462 GTP/Mg2+ binding site [chemical binding]; other site 358220005463 Switch I region; other site 358220005464 G2 box; other site 358220005465 Switch II region; other site 358220005466 G3 box; other site 358220005467 G4 box; other site 358220005468 G5 box; other site 358220005469 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 358220005470 G1 box; other site 358220005471 GTP/Mg2+ binding site [chemical binding]; other site 358220005472 Switch I region; other site 358220005473 G2 box; other site 358220005474 G3 box; other site 358220005475 Switch II region; other site 358220005476 G4 box; other site 358220005477 G5 box; other site 358220005478 bacterial Hfq-like; Region: Hfq; cd01716 358220005479 hexamer interface [polypeptide binding]; other site 358220005480 Sm1 motif; other site 358220005481 RNA binding site [nucleotide binding]; other site 358220005482 Sm2 motif; other site 358220005483 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 358220005484 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 358220005485 HflX GTPase family; Region: HflX; cd01878 358220005486 G1 box; other site 358220005487 GTP/Mg2+ binding site [chemical binding]; other site 358220005488 Switch I region; other site 358220005489 G2 box; other site 358220005490 G3 box; other site 358220005491 Switch II region; other site 358220005492 G4 box; other site 358220005493 G5 box; other site 358220005494 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 358220005495 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 358220005496 HflK protein; Region: hflK; TIGR01933 358220005497 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 358220005498 HflK protein; Region: hflK; TIGR01933 358220005499 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3242 358220005500 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 358220005501 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 358220005502 dimer interface [polypeptide binding]; other site 358220005503 motif 1; other site 358220005504 active site 358220005505 motif 2; other site 358220005506 motif 3; other site 358220005507 adenylosuccinate synthetase; Provisional; Region: PRK01117 358220005508 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 358220005509 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 358220005510 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 358220005511 active site 358220005512 uracil binding [chemical binding]; other site 358220005513 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 358220005514 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 358220005515 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 358220005516 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 358220005517 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 358220005518 active site 358220005519 NodB motif; other site 358220005520 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 358220005521 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 358220005522 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 358220005523 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 358220005524 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 358220005525 putative MPT binding site; other site 358220005526 glutamine synthetase; Provisional; Region: glnA; PRK09469 358220005527 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 358220005528 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 358220005529 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 358220005530 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220005531 dimer interface [polypeptide binding]; other site 358220005532 phosphorylation site [posttranslational modification] 358220005533 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220005534 ATP binding site [chemical binding]; other site 358220005535 Mg2+ binding site [ion binding]; other site 358220005536 G-X-G motif; other site 358220005537 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220005538 Response regulator receiver domain; Region: Response_reg; pfam00072 358220005539 active site 358220005540 phosphorylation site [posttranslational modification] 358220005541 intermolecular recognition site; other site 358220005542 dimerization interface [polypeptide binding]; other site 358220005543 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220005544 Walker A motif; other site 358220005545 ATP binding site [chemical binding]; other site 358220005546 Walker B motif; other site 358220005547 arginine finger; other site 358220005548 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 358220005549 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 358220005550 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 358220005551 putative catalytic site [active] 358220005552 putative phosphate binding site [ion binding]; other site 358220005553 active site 358220005554 metal binding site A [ion binding]; metal-binding site 358220005555 DNA binding site [nucleotide binding] 358220005556 putative AP binding site [nucleotide binding]; other site 358220005557 putative metal binding site B [ion binding]; other site 358220005558 Helix-turn-helix domain; Region: HTH_17; pfam12728 358220005559 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220005560 FeS/SAM binding site; other site 358220005561 Domain of unknown function (DUF4406); Region: DUF4406; pfam14359 358220005562 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 358220005563 HSP70 interaction site [polypeptide binding]; other site 358220005564 Uncharacterized conserved protein (DUF2303); Region: DUF2303; pfam10065 358220005565 KTSC domain; Region: KTSC; pfam13619 358220005566 ERF superfamily; Region: ERF; pfam04404 358220005567 ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation; Region: ASCH; cl01020 358220005568 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 358220005569 active site 358220005570 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 358220005571 Predicted transcriptional regulator [Transcription]; Region: COG2932 358220005572 Catalytic site [active] 358220005573 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; pfam09669 358220005574 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 358220005575 Terminase small subunit; Region: Terminase_2; pfam03592 358220005576 Terminase-like family; Region: Terminase_6; pfam03237 358220005577 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 358220005578 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 358220005579 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 358220005580 Methyltransferase domain; Region: Methyltransf_26; pfam13659 358220005581 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 358220005582 DEAD-like helicases superfamily; Region: DEXDc; smart00487 358220005583 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 358220005584 catalytic residue [active] 358220005585 Phage-related lysozyme (muraminidase) [General function prediction only]; Region: COG3772 358220005586 Phage protein (N4 Gp49/phage Sf6 gene 66) family; Region: Phage_gp49_66; pfam13876 358220005587 integrase; Provisional; Region: PRK09692 358220005588 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220005589 active site 358220005590 DNA binding site [nucleotide binding] 358220005591 Int/Topo IB signature motif; other site 358220005592 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 358220005593 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 358220005594 folate binding site [chemical binding]; other site 358220005595 NADP+ binding site [chemical binding]; other site 358220005596 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 358220005597 thymidylate synthase; Reviewed; Region: thyA; PRK01827 358220005598 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 358220005599 dimerization interface [polypeptide binding]; other site 358220005600 active site 358220005601 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 358220005602 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 358220005603 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 358220005604 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220005605 dimer interface [polypeptide binding]; other site 358220005606 conserved gate region; other site 358220005607 putative PBP binding loops; other site 358220005608 ABC-ATPase subunit interface; other site 358220005609 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 358220005610 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220005611 dimer interface [polypeptide binding]; other site 358220005612 conserved gate region; other site 358220005613 putative PBP binding loops; other site 358220005614 ABC-ATPase subunit interface; other site 358220005615 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 358220005616 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 358220005617 Walker A/P-loop; other site 358220005618 ATP binding site [chemical binding]; other site 358220005619 Q-loop/lid; other site 358220005620 ABC transporter signature motif; other site 358220005621 Walker B; other site 358220005622 D-loop; other site 358220005623 H-loop/switch region; other site 358220005624 TOBE domain; Region: TOBE_2; pfam08402 358220005625 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 358220005626 classical (c) SDRs; Region: SDR_c; cd05233 358220005627 NAD(P) binding site [chemical binding]; other site 358220005628 active site 358220005629 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 358220005630 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 358220005631 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 358220005632 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 358220005633 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 358220005634 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220005635 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220005636 Escherichia coli xylulokinase-like D-xylulose kinases; a subgroup of the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_EcXK-like; cd07808 358220005637 N- and C-terminal domain interface [polypeptide binding]; other site 358220005638 D-xylulose kinase; Region: XylB; TIGR01312 358220005639 active site 358220005640 MgATP binding site [chemical binding]; other site 358220005641 catalytic site [active] 358220005642 metal binding site [ion binding]; metal-binding site 358220005643 xylulose binding site [chemical binding]; other site 358220005644 homodimer interface [polypeptide binding]; other site 358220005645 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 358220005646 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 358220005647 putative substrate binding site [chemical binding]; other site 358220005648 putative ATP binding site [chemical binding]; other site 358220005649 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220005650 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 358220005651 Coenzyme A binding pocket [chemical binding]; other site 358220005652 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 358220005653 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 358220005654 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 358220005655 FAD binding domain; Region: FAD_binding_4; pfam01565 358220005656 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 358220005657 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 358220005658 Protein of unknown function (DUF962); Region: DUF962; cl01879 358220005659 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 358220005660 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 358220005661 nucleophilic elbow; other site 358220005662 catalytic triad; other site 358220005663 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK08134 358220005664 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 358220005665 homodimer interface [polypeptide binding]; other site 358220005666 substrate-cofactor binding pocket; other site 358220005667 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220005668 catalytic residue [active] 358220005669 FOG: CBS domain [General function prediction only]; Region: COG0517 358220005670 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 358220005671 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220005672 PAS domain; Region: PAS_9; pfam13426 358220005673 putative active site [active] 358220005674 heme pocket [chemical binding]; other site 358220005675 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220005676 GAF domain; Region: GAF; pfam01590 358220005677 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220005678 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220005679 metal binding site [ion binding]; metal-binding site 358220005680 active site 358220005681 I-site; other site 358220005682 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220005683 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 358220005684 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 358220005685 Tetramer interface [polypeptide binding]; other site 358220005686 active site 358220005687 FMN-binding site [chemical binding]; other site 358220005688 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 358220005689 Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain; Region: MPP_YhcR_N; cd07412 358220005690 putative active site [active] 358220005691 putative metal binding site [ion binding]; other site 358220005692 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 358220005693 EamA-like transporter family; Region: EamA; pfam00892 358220005694 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 358220005695 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 358220005696 ATP cone domain; Region: ATP-cone; pfam03477 358220005697 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 358220005698 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 358220005699 dimer interface [polypeptide binding]; other site 358220005700 active site 358220005701 glycine-pyridoxal phosphate binding site [chemical binding]; other site 358220005702 folate binding site [chemical binding]; other site 358220005703 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 358220005704 N-acetyl-D-glucosamine binding site [chemical binding]; other site 358220005705 catalytic residue [active] 358220005706 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 358220005707 putative transposase OrfB; Reviewed; Region: PHA02517 358220005708 Integrase core domain; Region: rve; pfam00665 358220005709 Integrase core domain; Region: rve_3; pfam13683 358220005710 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220005711 Homeodomain-like domain; Region: HTH_23; cl17451 358220005712 ribonuclease R; Region: RNase_R; TIGR02063 358220005713 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 358220005714 RNB domain; Region: RNB; pfam00773 358220005715 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 358220005716 RNA binding site [nucleotide binding]; other site 358220005717 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220005718 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 358220005719 Helix-turn-helix domain; Region: HTH_18; pfam12833 358220005720 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 358220005721 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 358220005722 putative substrate binding site [chemical binding]; other site 358220005723 putative ATP binding site [chemical binding]; other site 358220005724 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 358220005725 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 358220005726 hydroxyglutarate oxidase; Provisional; Region: PRK11728 358220005727 amidase; Provisional; Region: PRK07056 358220005728 Amidase; Region: Amidase; cl11426 358220005729 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of...; Region: RPS2; cd01425 358220005730 rRNA interaction site [nucleotide binding]; other site 358220005731 S8 interaction site; other site 358220005732 putative laminin-1 binding site; other site 358220005733 elongation factor Ts; Provisional; Region: tsf; PRK09377 358220005734 UBA/TS-N domain; Region: UBA; pfam00627 358220005735 Elongation factor TS; Region: EF_TS; pfam00889 358220005736 Elongation factor TS; Region: EF_TS; pfam00889 358220005737 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 358220005738 putative nucleotide binding site [chemical binding]; other site 358220005739 uridine monophosphate binding site [chemical binding]; other site 358220005740 homohexameric interface [polypeptide binding]; other site 358220005741 ribosome recycling factor; Reviewed; Region: frr; PRK00083 358220005742 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 358220005743 hinge region; other site 358220005744 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 358220005745 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 358220005746 catalytic residue [active] 358220005747 putative FPP diphosphate binding site; other site 358220005748 putative FPP binding hydrophobic cleft; other site 358220005749 dimer interface [polypeptide binding]; other site 358220005750 putative IPP diphosphate binding site; other site 358220005751 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 358220005752 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 358220005753 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 358220005754 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 358220005755 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 358220005756 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 358220005757 zinc metallopeptidase RseP; Provisional; Region: PRK10779 358220005758 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 358220005759 active site 358220005760 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 358220005761 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 358220005762 putative substrate binding region [chemical binding]; other site 358220005763 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 358220005764 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 358220005765 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 358220005766 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 358220005767 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 358220005768 Surface antigen; Region: Bac_surface_Ag; pfam01103 358220005769 periplasmic chaperone; Provisional; Region: PRK10780 358220005770 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 358220005771 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 358220005772 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 358220005773 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 358220005774 trimer interface [polypeptide binding]; other site 358220005775 active site 358220005776 UDP-GlcNAc binding site [chemical binding]; other site 358220005777 lipid binding site [chemical binding]; lipid-binding site 358220005778 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 358220005779 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 358220005780 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 358220005781 active site 358220005782 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 358220005783 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 358220005784 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 358220005785 RNA/DNA hybrid binding site [nucleotide binding]; other site 358220005786 active site 358220005787 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 358220005788 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 358220005789 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 358220005790 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 358220005791 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 358220005792 catalytic site [active] 358220005793 subunit interface [polypeptide binding]; other site 358220005794 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 358220005795 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 358220005796 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 358220005797 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 358220005798 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 358220005799 ATP-grasp domain; Region: ATP-grasp_4; cl17255 358220005800 MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate...; Region: MGS-like; cl00245 358220005801 substrate binding site [chemical binding]; other site 358220005802 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 358220005803 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 358220005804 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 358220005805 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 358220005806 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 358220005807 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 358220005808 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220005809 S-adenosylmethionine binding site [chemical binding]; other site 358220005810 FtsH Extracellular; Region: FtsH_ext; pfam06480 358220005811 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 358220005812 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220005813 Walker A motif; other site 358220005814 ATP binding site [chemical binding]; other site 358220005815 Walker B motif; other site 358220005816 arginine finger; other site 358220005817 Peptidase family M41; Region: Peptidase_M41; pfam01434 358220005818 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 358220005819 dihydropteroate synthase; Region: DHPS; TIGR01496 358220005820 substrate binding pocket [chemical binding]; other site 358220005821 dimer interface [polypeptide binding]; other site 358220005822 inhibitor binding site; inhibition site 358220005823 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 358220005824 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 358220005825 active site 358220005826 substrate binding site [chemical binding]; other site 358220005827 metal binding site [ion binding]; metal-binding site 358220005828 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220005829 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220005830 putative active site [active] 358220005831 heme pocket [chemical binding]; other site 358220005832 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220005833 putative active site [active] 358220005834 heme pocket [chemical binding]; other site 358220005835 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220005836 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220005837 metal binding site [ion binding]; metal-binding site 358220005838 active site 358220005839 I-site; other site 358220005840 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220005841 This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases; Region: CHASE; smart01079 358220005842 PAS domain; Region: PAS; smart00091 358220005843 PAS fold; Region: PAS_4; pfam08448 358220005844 putative active site [active] 358220005845 heme pocket [chemical binding]; other site 358220005846 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220005847 PAS domain; Region: PAS_9; pfam13426 358220005848 putative active site [active] 358220005849 heme pocket [chemical binding]; other site 358220005850 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220005851 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220005852 metal binding site [ion binding]; metal-binding site 358220005853 active site 358220005854 I-site; other site 358220005855 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220005856 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 358220005857 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 358220005858 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 358220005859 putative active site [active] 358220005860 putative metal binding site [ion binding]; other site 358220005861 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 358220005862 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 358220005863 polyphosphate kinase; Provisional; Region: PRK05443 358220005864 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 358220005865 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 358220005866 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 358220005867 putative active site [active] 358220005868 catalytic site [active] 358220005869 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 358220005870 putative domain interface [polypeptide binding]; other site 358220005871 putative active site [active] 358220005872 catalytic site [active] 358220005873 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 358220005874 catalytic core [active] 358220005875 guanosine pentaphosphate phosphohydrolase; Provisional; Region: PRK11031 358220005876 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 358220005877 PBP superfamily domain; Region: PBP_like_2; cl17296 358220005878 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 358220005879 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220005880 dimer interface [polypeptide binding]; other site 358220005881 conserved gate region; other site 358220005882 putative PBP binding loops; other site 358220005883 ABC-ATPase subunit interface; other site 358220005884 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 358220005885 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220005886 dimer interface [polypeptide binding]; other site 358220005887 conserved gate region; other site 358220005888 putative PBP binding loops; other site 358220005889 ABC-ATPase subunit interface; other site 358220005890 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 358220005891 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 358220005892 Walker A/P-loop; other site 358220005893 ATP binding site [chemical binding]; other site 358220005894 Q-loop/lid; other site 358220005895 ABC transporter signature motif; other site 358220005896 Walker B; other site 358220005897 D-loop; other site 358220005898 H-loop/switch region; other site 358220005899 transcriptional regulator PhoU; Provisional; Region: PRK11115 358220005900 PhoU domain; Region: PhoU; pfam01895 358220005901 PhoU domain; Region: PhoU; pfam01895 358220005902 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 358220005903 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220005904 active site 358220005905 phosphorylation site [posttranslational modification] 358220005906 intermolecular recognition site; other site 358220005907 dimerization interface [polypeptide binding]; other site 358220005908 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220005909 DNA binding site [nucleotide binding] 358220005910 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 358220005911 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220005912 putative active site [active] 358220005913 heme pocket [chemical binding]; other site 358220005914 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220005915 dimer interface [polypeptide binding]; other site 358220005916 phosphorylation site [posttranslational modification] 358220005917 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220005918 ATP binding site [chemical binding]; other site 358220005919 Mg2+ binding site [ion binding]; other site 358220005920 G-X-G motif; other site 358220005921 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 358220005922 putative efflux protein, MATE family; Region: matE; TIGR00797 358220005923 cation binding site [ion binding]; other site 358220005924 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 358220005925 transcription termination factor Rho; Provisional; Region: rho; PRK09376 358220005926 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 358220005927 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 358220005928 RNA binding site [nucleotide binding]; other site 358220005929 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 358220005930 multimer interface [polypeptide binding]; other site 358220005931 Walker A motif; other site 358220005932 ATP binding site [chemical binding]; other site 358220005933 Walker B motif; other site 358220005934 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 358220005935 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 358220005936 catalytic residues [active] 358220005937 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 358220005938 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 358220005939 AAA domain; Region: AAA_30; pfam13604 358220005940 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 358220005941 Family description; Region: UvrD_C_2; pfam13538 358220005942 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 358220005943 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 358220005944 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 358220005945 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220005946 Walker A motif; other site 358220005947 ATP binding site [chemical binding]; other site 358220005948 Walker B motif; other site 358220005949 arginine finger; other site 358220005950 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 358220005951 hypothetical protein; Validated; Region: PRK00153 358220005952 recombination protein RecR; Reviewed; Region: recR; PRK00076 358220005953 RecR protein; Region: RecR; pfam02132 358220005954 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 358220005955 putative active site [active] 358220005956 putative metal-binding site [ion binding]; other site 358220005957 tetramer interface [polypeptide binding]; other site 358220005958 MAPEG family; Region: MAPEG; cl09190 358220005959 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 358220005960 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 358220005961 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 358220005962 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 358220005963 N-acetyl-D-glucosamine binding site [chemical binding]; other site 358220005964 catalytic residue [active] 358220005965 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 358220005966 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 358220005967 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 358220005968 Methyltransferase domain; Region: Methyltransf_11; pfam08241 358220005969 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 358220005970 RNA/DNA hybrid binding site [nucleotide binding]; other site 358220005971 active site 358220005972 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 358220005973 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220005974 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220005975 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 358220005976 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 358220005977 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 358220005978 catalytic residues [active] 358220005979 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 358220005980 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 358220005981 dimer interface [polypeptide binding]; other site 358220005982 putative functional site; other site 358220005983 putative MPT binding site; other site 358220005984 Acetyltransferase (GNAT) domain; Region: Acetyltransf_4; pfam13420 358220005985 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220005986 Coenzyme A binding pocket [chemical binding]; other site 358220005987 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 358220005988 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 358220005989 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 358220005990 GTP binding site; other site 358220005991 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 358220005992 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220005993 FeS/SAM binding site; other site 358220005994 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 358220005995 Sensors of blue-light using FAD; Region: BLUF; pfam04940 358220005996 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 358220005997 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 358220005998 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220005999 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 358220006000 NAD(P) binding site [chemical binding]; other site 358220006001 active site 358220006002 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 358220006003 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 358220006004 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like; Region: ALDH_AAS00426; cd07109 358220006005 NAD(P) binding site [chemical binding]; other site 358220006006 catalytic residues [active] 358220006007 catalytic residues [active] 358220006008 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220006009 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220006010 ligand binding site [chemical binding]; other site 358220006011 flexible hinge region; other site 358220006012 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 358220006013 non-specific DNA interactions [nucleotide binding]; other site 358220006014 DNA binding site [nucleotide binding] 358220006015 sequence specific DNA binding site [nucleotide binding]; other site 358220006016 putative cAMP binding site [chemical binding]; other site 358220006017 Predicted membrane protein [Function unknown]; Region: COG4539 358220006018 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 358220006019 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 358220006020 ABC-2 type transporter; Region: ABC2_membrane; cl17235 358220006021 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 358220006022 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 358220006023 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220006024 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220006025 potential frameshift: common BLAST hit: gi|160900004|ref|YP_001565586.1| outer membrane efflux protein 358220006026 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 358220006027 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 358220006028 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220006029 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220006030 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 358220006031 dimer interface [polypeptide binding]; other site 358220006032 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220006033 metal binding site [ion binding]; metal-binding site 358220006034 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 358220006035 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220006036 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220006037 motif II; other site 358220006038 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 358220006039 Rubredoxin [Energy production and conversion]; Region: COG1773 358220006040 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 358220006041 iron binding site [ion binding]; other site 358220006042 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 358220006043 Dihaem cytochrome c; Region: DHC; pfam09626 358220006044 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 358220006045 Predicted membrane protein [Function unknown]; Region: COG3212 358220006046 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220006047 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220006048 active site 358220006049 phosphorylation site [posttranslational modification] 358220006050 intermolecular recognition site; other site 358220006051 dimerization interface [polypeptide binding]; other site 358220006052 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220006053 DNA binding site [nucleotide binding] 358220006054 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220006055 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220006056 ATP binding site [chemical binding]; other site 358220006057 Mg2+ binding site [ion binding]; other site 358220006058 G-X-G motif; other site 358220006059 putative transposase OrfB; Reviewed; Region: PHA02517 358220006060 Integrase core domain; Region: rve; pfam00665 358220006061 Integrase core domain; Region: rve_3; pfam13683 358220006062 Homeodomain-like domain; Region: HTH_23; cl17451 358220006063 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 358220006064 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 358220006065 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 358220006066 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 358220006067 dimer interface [polypeptide binding]; other site 358220006068 substrate binding site [chemical binding]; other site 358220006069 metal binding sites [ion binding]; metal-binding site 358220006070 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220006071 HAMP domain; Region: HAMP; pfam00672 358220006072 dimerization interface [polypeptide binding]; other site 358220006073 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220006074 dimer interface [polypeptide binding]; other site 358220006075 putative CheW interface [polypeptide binding]; other site 358220006076 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220006077 PGAP1-like protein; Region: PGAP1; pfam07819 358220006078 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 358220006079 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220006080 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220006081 dimerization interface [polypeptide binding]; other site 358220006082 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220006083 dimer interface [polypeptide binding]; other site 358220006084 putative CheW interface [polypeptide binding]; other site 358220006085 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220006086 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 358220006087 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220006088 dimerization interface [polypeptide binding]; other site 358220006089 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220006090 dimer interface [polypeptide binding]; other site 358220006091 putative CheW interface [polypeptide binding]; other site 358220006092 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220006093 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 358220006094 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220006095 dimerization interface [polypeptide binding]; other site 358220006096 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220006097 dimer interface [polypeptide binding]; other site 358220006098 putative CheW interface [polypeptide binding]; other site 358220006099 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 358220006100 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 358220006101 Protein of unknown function, DUF482; Region: DUF482; pfam04339 358220006102 NAD synthetase; Provisional; Region: PRK13981 358220006103 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 358220006104 multimer interface [polypeptide binding]; other site 358220006105 active site 358220006106 catalytic triad [active] 358220006107 protein interface 1 [polypeptide binding]; other site 358220006108 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 358220006109 homodimer interface [polypeptide binding]; other site 358220006110 NAD binding pocket [chemical binding]; other site 358220006111 ATP binding pocket [chemical binding]; other site 358220006112 Mg binding site [ion binding]; other site 358220006113 active-site loop [active] 358220006114 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 358220006115 Nitrogen regulatory protein P-II; Region: P-II; smart00938 358220006116 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 358220006117 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 358220006118 RDD family; Region: RDD; pfam06271 358220006119 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 358220006120 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 358220006121 RNA polymerase factor sigma-70; Validated; Region: PRK09047 358220006122 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220006123 DNA binding residues [nucleotide binding] 358220006124 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 358220006125 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 358220006126 PYR/PP interface [polypeptide binding]; other site 358220006127 dimer interface [polypeptide binding]; other site 358220006128 TPP binding site [chemical binding]; other site 358220006129 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 358220006130 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 358220006131 TPP-binding site [chemical binding]; other site 358220006132 dimer interface [polypeptide binding]; other site 358220006133 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 358220006134 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 358220006135 putative valine binding site [chemical binding]; other site 358220006136 dimer interface [polypeptide binding]; other site 358220006137 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 358220006138 ketol-acid reductoisomerase; Provisional; Region: PRK05479 358220006139 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 358220006140 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 358220006141 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 358220006142 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 358220006143 2-isopropylmalate synthase; Validated; Region: PRK00915 358220006144 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 358220006145 active site 358220006146 catalytic residues [active] 358220006147 metal binding site [ion binding]; metal-binding site 358220006148 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 358220006149 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 358220006150 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 358220006151 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 358220006152 Transcriptional regulator [Transcription]; Region: IclR; COG1414 358220006153 Bacterial transcriptional regulator; Region: IclR; pfam01614 358220006154 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 358220006155 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 358220006156 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 358220006157 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 358220006158 MASE2 domain; Region: MASE2; pfam05230 358220006159 Protein of unknown function (DUF2829); Region: DUF2829; pfam11195 358220006160 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 358220006161 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cl17512 358220006162 beta-clamp/clamp loader binding surface; other site 358220006163 beta-clamp/translesion DNA polymerase binding surface; other site 358220006164 HTH domain; Region: HTH_11; cl17392 358220006165 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 358220006166 Ligand Binding Site [chemical binding]; other site 358220006167 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 358220006168 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 358220006169 Phage related hypothetical protein (DUF1799); Region: DUF1799; pfam08809 358220006170 Phage-related minor tail protein [Function unknown]; Region: COG5281 358220006171 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 358220006172 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 358220006173 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 358220006174 catalytic residue [active] 358220006175 Phage regulatory protein CII (CP76); Region: Phage_CP76; pfam06892 358220006176 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 358220006177 active site 358220006178 catalytic residues [active] 358220006179 DNA binding site [nucleotide binding] 358220006180 Int/Topo IB signature motif; other site 358220006181 Domain of unknown function (DUF4406); Region: DUF4406; pfam14359 358220006182 DNA primase domain-containing protein; Region: PHA02415 358220006183 CHC2 zinc finger; Region: zf-CHC2; cl17510 358220006184 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 358220006185 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220006186 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 358220006187 active site 358220006188 DNA binding site [nucleotide binding] 358220006189 Int/Topo IB signature motif; other site 358220006190 Sm and related proteins; Region: Sm_like; cl00259 358220006191 RNA binding site [nucleotide binding]; other site 358220006192 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 358220006193 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 358220006194 catalytic residues [active] 358220006195 catalytic nucleophile [active] 358220006196 Recombinase; Region: Recombinase; pfam07508 358220006197 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 358220006198 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 358220006199 active site 358220006200 catalytic residues [active] 358220006201 metal binding site [ion binding]; metal-binding site 358220006202 PII uridylyl-transferase; Provisional; Region: PRK03059 358220006203 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 358220006204 metal binding triad; other site 358220006205 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 358220006206 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220006207 Zn2+ binding site [ion binding]; other site 358220006208 Mg2+ binding site [ion binding]; other site 358220006209 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 358220006210 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 358220006211 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 358220006212 active site 358220006213 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 358220006214 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 358220006215 dimerization interface [polypeptide binding]; other site 358220006216 ATP binding site [chemical binding]; other site 358220006217 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 358220006218 dimerization interface [polypeptide binding]; other site 358220006219 ATP binding site [chemical binding]; other site 358220006220 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 358220006221 putative active site [active] 358220006222 catalytic triad [active] 358220006223 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 358220006224 [2Fe-2S] cluster binding site [ion binding]; other site 358220006225 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 358220006226 inter-subunit interface; other site 358220006227 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 358220006228 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 358220006229 iron-sulfur cluster [ion binding]; other site 358220006230 [2Fe-2S] cluster binding site [ion binding]; other site 358220006231 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 358220006232 putative alpha subunit interface [polypeptide binding]; other site 358220006233 putative active site [active] 358220006234 putative substrate binding site [chemical binding]; other site 358220006235 Fe binding site [ion binding]; other site 358220006236 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 358220006237 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220006238 catalytic loop [active] 358220006239 iron binding site [ion binding]; other site 358220006240 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S]...; Region: O2ase_reductase_like; cd06187 358220006241 FAD binding pocket [chemical binding]; other site 358220006242 FAD binding motif [chemical binding]; other site 358220006243 phosphate binding motif [ion binding]; other site 358220006244 beta-alpha-beta structure motif; other site 358220006245 NAD binding pocket [chemical binding]; other site 358220006246 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 358220006247 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006248 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 358220006249 substrate binding pocket [chemical binding]; other site 358220006250 dimerization interface [polypeptide binding]; other site 358220006251 Protein of unknown function (DUF808); Region: DUF808; pfam05661 358220006252 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 358220006253 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 358220006254 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 358220006255 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 358220006256 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 358220006257 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 358220006258 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 358220006259 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 358220006260 homodimer interface [polypeptide binding]; other site 358220006261 substrate-cofactor binding pocket; other site 358220006262 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220006263 catalytic residue [active] 358220006264 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 358220006265 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 358220006266 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220006267 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 358220006268 Soluble P-type ATPase [General function prediction only]; Region: COG4087 358220006269 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 358220006270 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 358220006271 Peptidase family U32; Region: Peptidase_U32; pfam01136 358220006272 Collagenase; Region: DUF3656; pfam12392 358220006273 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220006274 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 358220006275 dimerization interface [polypeptide binding]; other site 358220006276 ligand binding site [chemical binding]; other site 358220006277 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 358220006278 nucleoside/Zn binding site; other site 358220006279 dimer interface [polypeptide binding]; other site 358220006280 catalytic motif [active] 358220006281 haloalkane dehalogenase; Provisional; Region: PRK00870 358220006282 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 358220006283 dimer interface [polypeptide binding]; other site 358220006284 catalytic triad [active] 358220006285 cyclase homology domain; Region: CHD; cd07302 358220006286 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 358220006287 nucleotidyl binding site; other site 358220006288 metal binding site [ion binding]; metal-binding site 358220006289 dimer interface [polypeptide binding]; other site 358220006290 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 358220006291 phosphopeptide binding site; other site 358220006292 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 358220006293 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 358220006294 active site 358220006295 L-asparaginase II; Region: Asparaginase_II; pfam06089 358220006296 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220006297 Acyl-CoA dehydrogenases similar to fadE2; Region: ACAD_FadE2; cd01155 358220006298 FAD binding site [chemical binding]; other site 358220006299 substrate binding site [chemical binding]; other site 358220006300 catalytic base [active] 358220006301 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 358220006302 Phosphotransferase enzyme family; Region: APH; pfam01636 358220006303 putative active site [active] 358220006304 putative substrate binding site [chemical binding]; other site 358220006305 ATP binding site [chemical binding]; other site 358220006306 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220006307 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220006308 ligand binding site [chemical binding]; other site 358220006309 flexible hinge region; other site 358220006310 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 358220006311 enoyl-CoA hydratase; Provisional; Region: PRK07511 358220006312 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220006313 substrate binding site [chemical binding]; other site 358220006314 oxyanion hole (OAH) forming residues; other site 358220006315 trimer interface [polypeptide binding]; other site 358220006316 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 358220006317 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220006318 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220006319 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220006320 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 358220006321 thiamine phosphate binding site [chemical binding]; other site 358220006322 active site 358220006323 pyrophosphate binding site [ion binding]; other site 358220006324 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 358220006325 ThiS interaction site; other site 358220006326 putative active site [active] 358220006327 tetramer interface [polypeptide binding]; other site 358220006328 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 358220006329 thiS-thiF/thiG interaction site; other site 358220006330 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220006331 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 358220006332 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 358220006333 dimer interface [polypeptide binding]; other site 358220006334 substrate binding site [chemical binding]; other site 358220006335 ATP binding site [chemical binding]; other site 358220006336 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 358220006337 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 358220006338 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 358220006339 Ferredoxin [Energy production and conversion]; Region: COG1146 358220006340 4Fe-4S binding domain; Region: Fer4; cl02805 358220006341 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 358220006342 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 358220006343 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 358220006344 G1 box; other site 358220006345 GTP/Mg2+ binding site [chemical binding]; other site 358220006346 G2 box; other site 358220006347 Switch I region; other site 358220006348 G3 box; other site 358220006349 Switch II region; other site 358220006350 G4 box; other site 358220006351 G5 box; other site 358220006352 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 358220006353 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 358220006354 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 358220006355 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 358220006356 Active Sites [active] 358220006357 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 358220006358 Active Sites [active] 358220006359 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 358220006360 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 358220006361 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 358220006362 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 358220006363 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 358220006364 Uncharacterized conserved protein [Function unknown]; Region: COG4121 358220006365 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 358220006366 oxidative damage protection protein; Provisional; Region: PRK05408 358220006367 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 358220006368 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 358220006369 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 358220006370 FMN reductase, SsuE family; Region: FMN_reduc_SsuE; TIGR03567 358220006371 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 358220006372 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220006373 substrate binding pocket [chemical binding]; other site 358220006374 membrane-bound complex binding site; other site 358220006375 hinge residues; other site 358220006376 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 358220006377 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 358220006378 active site 358220006379 dimer interface [polypeptide binding]; other site 358220006380 non-prolyl cis peptide bond; other site 358220006381 insertion regions; other site 358220006382 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 358220006383 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220006384 active site 358220006385 metal binding site [ion binding]; metal-binding site 358220006386 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 358220006387 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220006388 putative PBP binding loops; other site 358220006389 dimer interface [polypeptide binding]; other site 358220006390 ABC-ATPase subunit interface; other site 358220006391 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 358220006392 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 358220006393 Walker A/P-loop; other site 358220006394 ATP binding site [chemical binding]; other site 358220006395 Q-loop/lid; other site 358220006396 ABC transporter signature motif; other site 358220006397 Walker B; other site 358220006398 D-loop; other site 358220006399 H-loop/switch region; other site 358220006400 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 358220006401 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 358220006402 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 358220006403 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 358220006404 Ligand Binding Site [chemical binding]; other site 358220006405 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 358220006406 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 358220006407 active site 358220006408 non-prolyl cis peptide bond; other site 358220006409 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 358220006410 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 358220006411 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 358220006412 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220006413 substrate binding pocket [chemical binding]; other site 358220006414 membrane-bound complex binding site; other site 358220006415 hinge residues; other site 358220006416 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 358220006417 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220006418 ABC-ATPase subunit interface; other site 358220006419 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 358220006420 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220006421 dimer interface [polypeptide binding]; other site 358220006422 conserved gate region; other site 358220006423 putative PBP binding loops; other site 358220006424 ABC-ATPase subunit interface; other site 358220006425 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 358220006426 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 358220006427 Walker A/P-loop; other site 358220006428 ATP binding site [chemical binding]; other site 358220006429 Q-loop/lid; other site 358220006430 ABC transporter signature motif; other site 358220006431 Walker B; other site 358220006432 D-loop; other site 358220006433 H-loop/switch region; other site 358220006434 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 358220006435 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 358220006436 substrate binding pocket [chemical binding]; other site 358220006437 membrane-bound complex binding site; other site 358220006438 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 358220006439 Sulfatase; Region: Sulfatase; pfam00884 358220006440 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12683 358220006441 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006442 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 358220006443 substrate binding site [chemical binding]; other site 358220006444 dimerization interface [polypeptide binding]; other site 358220006445 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 358220006446 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006447 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220006448 dimerization interface [polypeptide binding]; other site 358220006449 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 358220006450 tetramer interface [polypeptide binding]; other site 358220006451 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 358220006452 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006453 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220006454 dimerization interface [polypeptide binding]; other site 358220006455 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220006456 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006457 LysR substrate binding domain; Region: LysR_substrate; pfam03466 358220006458 dimerization interface [polypeptide binding]; other site 358220006459 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR6; cd08272 358220006460 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 358220006461 putative NAD(P) binding site [chemical binding]; other site 358220006462 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220006463 Helix-turn-helix domain; Region: HTH_38; pfam13936 358220006464 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220006465 Integrase core domain; Region: rve; pfam00665 358220006466 Integrase core domain; Region: rve_3; cl15866 358220006467 Flagellin N-methylase; Region: FliB; pfam03692 358220006468 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 358220006469 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220006470 dimer interface [polypeptide binding]; other site 358220006471 phosphorylation site [posttranslational modification] 358220006472 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220006473 ATP binding site [chemical binding]; other site 358220006474 Mg2+ binding site [ion binding]; other site 358220006475 G-X-G motif; other site 358220006476 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220006477 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220006478 active site 358220006479 phosphorylation site [posttranslational modification] 358220006480 intermolecular recognition site; other site 358220006481 dimerization interface [polypeptide binding]; other site 358220006482 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220006483 DNA binding site [nucleotide binding] 358220006484 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 358220006485 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 358220006486 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 358220006487 DEAD_2; Region: DEAD_2; pfam06733 358220006488 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 358220006489 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 358220006490 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220006491 active site 358220006492 DNA binding site [nucleotide binding] 358220006493 Int/Topo IB signature motif; other site 358220006494 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220006495 active site 358220006496 DNA binding site [nucleotide binding] 358220006497 Int/Topo IB signature motif; other site 358220006498 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 358220006499 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 358220006500 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases; Region: INT_SG5; cd01190 358220006501 Int/Topo IB signature motif; other site 358220006502 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 358220006503 active site 358220006504 NTP binding site [chemical binding]; other site 358220006505 metal binding triad [ion binding]; metal-binding site 358220006506 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 358220006507 galactonate dehydratase; Provisional; Region: PRK14017 358220006508 D-galactonate dehydratase catalyses the dehydration of galactonate to 2-keto-3-deoxygalactnate (KDGal), as part of the D-galactonate nonphosphorolytic catabolic Entner-Doudoroff pathway. D-galactonate dehydratase belongs to the enolase superfamily of...; Region: D-galactonate_dehydratase; cd03325 358220006509 putative active site pocket [active] 358220006510 putative metal binding site [ion binding]; other site 358220006511 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 358220006512 active site 358220006513 intersubunit interface [polypeptide binding]; other site 358220006514 catalytic residue [active] 358220006515 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism]; Region: DgoK; COG3734 358220006516 2-keto-3-deoxy-galactonokinase; Region: DGOK; pfam05035 358220006517 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 358220006518 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 358220006519 inhibitor site; inhibition site 358220006520 active site 358220006521 dimer interface [polypeptide binding]; other site 358220006522 catalytic residue [active] 358220006523 dihydroxy-acid dehydratase; Validated; Region: PRK06131 358220006524 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220006525 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 358220006526 TM-ABC transporter signature motif; other site 358220006527 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220006528 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 358220006529 TM-ABC transporter signature motif; other site 358220006530 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 358220006531 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 358220006532 Walker A/P-loop; other site 358220006533 ATP binding site [chemical binding]; other site 358220006534 Q-loop/lid; other site 358220006535 ABC transporter signature motif; other site 358220006536 Walker B; other site 358220006537 D-loop; other site 358220006538 H-loop/switch region; other site 358220006539 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 358220006540 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220006541 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 358220006542 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 358220006543 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220006544 TM-ABC transporter signature motif; other site 358220006545 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 358220006546 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 358220006547 Walker A/P-loop; other site 358220006548 ATP binding site [chemical binding]; other site 358220006549 Q-loop/lid; other site 358220006550 ABC transporter signature motif; other site 358220006551 Walker B; other site 358220006552 D-loop; other site 358220006553 H-loop/switch region; other site 358220006554 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 358220006555 ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: XylF; COG4213 358220006556 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 358220006557 putative ligand binding site [chemical binding]; other site 358220006558 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 358220006559 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 358220006560 putative ligand binding site [chemical binding]; other site 358220006561 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 358220006562 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 358220006563 NAD(P) binding site [chemical binding]; other site 358220006564 catalytic residues [active] 358220006565 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 358220006566 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006567 The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Region: PBP2_GbpR; cd08435 358220006568 putative dimerization interface [polypeptide binding]; other site 358220006569 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 358220006570 classical (c) SDRs; Region: SDR_c; cd05233 358220006571 NAD(P) binding site [chemical binding]; other site 358220006572 active site 358220006573 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 358220006574 aldose 1-epimerase, similar to Escherichia coli YphB; Region: Aldose_epim_Ec_YphB; cd09021 358220006575 active site 358220006576 catalytic residues [active] 358220006577 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 358220006578 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220006579 Domain of unknown function (DU1801); Region: DUF1801; cl17490 358220006580 Domain of unknown function (DU1801); Region: DUF1801; cl17490 358220006581 hypothetical protein; Provisional; Region: PRK06126 358220006582 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220006583 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220006584 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220006585 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220006586 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006587 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 358220006588 putative dimerization interface [polypeptide binding]; other site 358220006589 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09775 358220006590 HipA-like N-terminal domain; Region: HipA_N; pfam07805 358220006591 HipA-like C-terminal domain; Region: HipA_C; pfam07804 358220006592 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220006593 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006594 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220006595 putative effector binding pocket; other site 358220006596 dimerization interface [polypeptide binding]; other site 358220006597 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 358220006598 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220006599 putative substrate translocation pore; other site 358220006600 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 358220006601 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 358220006602 Walker A/P-loop; other site 358220006603 ATP binding site [chemical binding]; other site 358220006604 Q-loop/lid; other site 358220006605 ABC transporter signature motif; other site 358220006606 Walker B; other site 358220006607 D-loop; other site 358220006608 H-loop/switch region; other site 358220006609 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 358220006610 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220006611 dimer interface [polypeptide binding]; other site 358220006612 conserved gate region; other site 358220006613 ABC-ATPase subunit interface; other site 358220006614 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220006615 Coenzyme A binding pocket [chemical binding]; other site 358220006616 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220006617 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 358220006618 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 358220006619 MOFRL family; Region: MOFRL; pfam05161 358220006620 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 358220006621 tartrate dehydrogenase; Region: TTC; TIGR02089 358220006622 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220006623 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006624 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 358220006625 putative effector binding pocket; other site 358220006626 putative dimerization interface [polypeptide binding]; other site 358220006627 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 358220006628 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 358220006629 Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Region: HTH_YyaN; cd01109 358220006630 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 358220006631 DNA binding residues [nucleotide binding] 358220006632 putative dimer interface [polypeptide binding]; other site 358220006633 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 358220006634 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 358220006635 NAD(P) binding site [chemical binding]; other site 358220006636 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 358220006637 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 358220006638 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 358220006639 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 358220006640 RNA binding site [nucleotide binding]; other site 358220006641 HDOD domain; Region: HDOD; pfam08668 358220006642 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 358220006643 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220006644 dimerization interface [polypeptide binding]; other site 358220006645 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220006646 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220006647 putative active site [active] 358220006648 heme pocket [chemical binding]; other site 358220006649 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220006650 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220006651 metal binding site [ion binding]; metal-binding site 358220006652 active site 358220006653 I-site; other site 358220006654 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220006655 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 358220006656 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 358220006657 putative active site [active] 358220006658 metal binding site [ion binding]; metal-binding site 358220006659 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 358220006660 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 358220006661 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 358220006662 substrate binding pocket [chemical binding]; other site 358220006663 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 358220006664 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 358220006665 active site 358220006666 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 358220006667 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 358220006668 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 358220006669 YceG-like family; Region: YceG; pfam02618 358220006670 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 358220006671 dimerization interface [polypeptide binding]; other site 358220006672 thymidylate kinase; Validated; Region: tmk; PRK00698 358220006673 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 358220006674 TMP-binding site; other site 358220006675 ATP-binding site [chemical binding]; other site 358220006676 DNA polymerase III subunit delta'; Validated; Region: PRK06964 358220006677 DNA polymerase III subunit delta'; Validated; Region: PRK08485 358220006678 PilZ domain; Region: PilZ; cl01260 358220006679 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 358220006680 active site 358220006681 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 358220006682 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 358220006683 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 358220006684 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 358220006685 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 358220006686 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 358220006687 Walker A/P-loop; other site 358220006688 ATP binding site [chemical binding]; other site 358220006689 Q-loop/lid; other site 358220006690 ABC transporter signature motif; other site 358220006691 Walker B; other site 358220006692 D-loop; other site 358220006693 H-loop/switch region; other site 358220006694 translocation protein TolB; Provisional; Region: tolB; PRK02889 358220006695 TolB amino-terminal domain; Region: TolB_N; pfam04052 358220006696 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 358220006697 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 358220006698 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 358220006699 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 358220006700 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 358220006701 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 358220006702 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 358220006703 ligand binding site [chemical binding]; other site 358220006704 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 358220006705 Tetratricopeptide repeat; Region: TPR_6; pfam13174 358220006706 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 358220006707 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 358220006708 putative ATP binding site [chemical binding]; other site 358220006709 putative substrate interface [chemical binding]; other site 358220006710 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 358220006711 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220006712 active site 358220006713 DNA binding site [nucleotide binding] 358220006714 Int/Topo IB signature motif; other site 358220006715 Helix-turn-helix domain; Region: HTH_17; cl17695 358220006716 HNH endonuclease; Region: HNH_3; pfam13392 358220006717 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor...; Region: AP2; cl00033 358220006718 Domain of unknown function (DUF4406); Region: DUF4406; pfam14359 358220006719 ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation; Region: ASCH; cl01020 358220006720 recombination associated protein; Reviewed; Region: rdgC; PRK00321 358220006721 Siphovirus Gp157; Region: Sipho_Gp157; pfam05565 358220006722 AAA domain; Region: AAA_22; pfam13401 358220006723 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 358220006724 catalytic residue [active] 358220006725 Toxin YafO, type II toxin-antitoxin system; Region: YafO_toxin; cl08066 358220006726 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 358220006727 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220006728 non-specific DNA binding site [nucleotide binding]; other site 358220006729 sequence-specific DNA binding site [nucleotide binding]; other site 358220006730 salt bridge; other site 358220006731 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 358220006732 beta-adaptin; Provisional; Region: PTZ00429 358220006733 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 358220006734 active site 358220006735 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 358220006736 Domain of unknown function DUF20; Region: UPF0118; pfam01594 358220006737 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 358220006738 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 358220006739 TPP-binding site [chemical binding]; other site 358220006740 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 358220006741 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 358220006742 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 358220006743 E3 interaction surface; other site 358220006744 lipoyl attachment site [posttranslational modification]; other site 358220006745 e3 binding domain; Region: E3_binding; pfam02817 358220006746 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 358220006747 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 358220006748 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220006749 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 358220006750 Predicted ATPase [General function prediction only]; Region: COG1485 358220006751 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 358220006752 active site 358220006753 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 358220006754 DEAD/DEAH box helicase; Region: DEAD; pfam00270 358220006755 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 358220006756 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 358220006757 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 358220006758 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 358220006759 putative active site [active] 358220006760 putative PHP Thumb interface [polypeptide binding]; other site 358220006761 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 358220006762 generic binding surface II; other site 358220006763 generic binding surface I; other site 358220006764 Uncharacterized conserved protein [Function unknown]; Region: COG2127 358220006765 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 358220006766 Clp amino terminal domain; Region: Clp_N; pfam02861 358220006767 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220006768 Walker A motif; other site 358220006769 ATP binding site [chemical binding]; other site 358220006770 Walker B motif; other site 358220006771 arginine finger; other site 358220006772 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220006773 Walker A motif; other site 358220006774 ATP binding site [chemical binding]; other site 358220006775 Walker B motif; other site 358220006776 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 358220006777 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 358220006778 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 358220006779 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 358220006780 Pseudouridine synthase, a subgroup of the RluA family; Region: PSRA_1; cd02558 358220006781 probable active site [active] 358220006782 succinic semialdehyde dehydrogenase; Region: PLN02278 358220006783 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 358220006784 tetramerization interface [polypeptide binding]; other site 358220006785 NAD(P) binding site [chemical binding]; other site 358220006786 catalytic residues [active] 358220006787 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 358220006788 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220006789 dimer interface [polypeptide binding]; other site 358220006790 conserved gate region; other site 358220006791 putative PBP binding loops; other site 358220006792 ABC-ATPase subunit interface; other site 358220006793 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220006794 dimer interface [polypeptide binding]; other site 358220006795 conserved gate region; other site 358220006796 putative PBP binding loops; other site 358220006797 ABC-ATPase subunit interface; other site 358220006798 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 358220006799 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 358220006800 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 358220006801 ATP-binding cassette domain of the polyamine transporter; Region: ABC_PotA_N; cd03300 358220006802 Walker A/P-loop; other site 358220006803 ATP binding site [chemical binding]; other site 358220006804 Q-loop/lid; other site 358220006805 ABC transporter signature motif; other site 358220006806 Walker B; other site 358220006807 D-loop; other site 358220006808 H-loop/switch region; other site 358220006809 TOBE domain; Region: TOBE_2; pfam08402 358220006810 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 358220006811 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 358220006812 inhibitor-cofactor binding pocket; inhibition site 358220006813 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220006814 catalytic residue [active] 358220006815 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 358220006816 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220006817 DNA-binding site [nucleotide binding]; DNA binding site 358220006818 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220006819 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220006820 homodimer interface [polypeptide binding]; other site 358220006821 catalytic residue [active] 358220006822 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220006823 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220006824 DNA-binding site [nucleotide binding]; DNA binding site 358220006825 FCD domain; Region: FCD; pfam07729 358220006826 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220006827 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 358220006828 DctM-like transporters; Region: DctM; pfam06808 358220006829 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 358220006830 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 358220006831 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 358220006832 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_4; pfam13510 358220006833 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 358220006834 hydroxyproline-2-epimerase; Provisional; Region: PRK13970 358220006835 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 358220006836 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 358220006837 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 358220006838 inhibitor site; inhibition site 358220006839 active site 358220006840 dimer interface [polypeptide binding]; other site 358220006841 catalytic residue [active] 358220006842 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 358220006843 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 358220006844 motif 1; other site 358220006845 active site 358220006846 motif 2; other site 358220006847 motif 3; other site 358220006848 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 358220006849 Cache domain; Region: Cache_1; pfam02743 358220006850 GAF domain; Region: GAF_3; pfam13492 358220006851 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220006852 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220006853 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220006854 metal binding site [ion binding]; metal-binding site 358220006855 active site 358220006856 I-site; other site 358220006857 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220006858 S-adenosylmethionine binding site [chemical binding]; other site 358220006859 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 358220006860 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 358220006861 active site 358220006862 HIGH motif; other site 358220006863 nucleotide binding site [chemical binding]; other site 358220006864 active site 358220006865 KMSKS motif; other site 358220006866 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 358220006867 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 358220006868 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006869 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 358220006870 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220006871 dimerization interface [polypeptide binding]; other site 358220006872 Pirin-related protein [General function prediction only]; Region: COG1741 358220006873 Pirin; Region: Pirin; pfam02678 358220006874 DoxX; Region: DoxX; pfam07681 358220006875 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 358220006876 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 358220006877 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 358220006878 Pirin-related protein [General function prediction only]; Region: COG1741 358220006879 Pirin; Region: Pirin; pfam02678 358220006880 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 358220006881 rhodanese superfamily protein; Provisional; Region: PRK05320 358220006882 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 358220006883 active site residue [active] 358220006884 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 358220006885 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 358220006886 P-loop; other site 358220006887 ADP binding residues [chemical binding]; other site 358220006888 Switch I; other site 358220006889 Switch II; other site 358220006890 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220006891 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220006892 metal binding site [ion binding]; metal-binding site 358220006893 active site 358220006894 I-site; other site 358220006895 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 358220006896 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 358220006897 Sulfate transporter family; Region: Sulfate_transp; pfam00916 358220006898 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 358220006899 BON domain; Region: BON; pfam04972 358220006900 cystathionine beta-lyase; Provisional; Region: PRK07050 358220006901 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 358220006902 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220006903 catalytic residue [active] 358220006904 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 358220006905 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 358220006906 active site 358220006907 catalytic triad [active] 358220006908 oxyanion hole [active] 358220006909 switch loop; other site 358220006910 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 358220006911 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 358220006912 Walker A/P-loop; other site 358220006913 ATP binding site [chemical binding]; other site 358220006914 Q-loop/lid; other site 358220006915 ABC transporter signature motif; other site 358220006916 Walker B; other site 358220006917 D-loop; other site 358220006918 H-loop/switch region; other site 358220006919 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 358220006920 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 358220006921 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 358220006922 NAD-dependent deacetylase; Provisional; Region: PRK00481 358220006923 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 358220006924 NAD+ binding site [chemical binding]; other site 358220006925 substrate binding site [chemical binding]; other site 358220006926 Zn binding site [ion binding]; other site 358220006927 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220006928 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220006929 putative ligand binding site [chemical binding]; other site 358220006930 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 358220006931 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 358220006932 active site 358220006933 catalytic tetrad [active] 358220006934 Chromate transporter; Region: Chromate_transp; pfam02417 358220006935 Chromate transporter; Region: Chromate_transp; pfam02417 358220006936 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 358220006937 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 358220006938 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 358220006939 HipA N-terminal domain; Region: Couple_hipA; pfam13657 358220006940 HipA-like N-terminal domain; Region: HipA_N; pfam07805 358220006941 HipA-like C-terminal domain; Region: HipA_C; pfam07804 358220006942 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220006943 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 358220006944 non-specific DNA binding site [nucleotide binding]; other site 358220006945 salt bridge; other site 358220006946 sequence-specific DNA binding site [nucleotide binding]; other site 358220006947 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220006948 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220006949 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 358220006950 dimerization interface [polypeptide binding]; other site 358220006951 substrate binding pocket [chemical binding]; other site 358220006952 D-serine dehydratase; Provisional; Region: PRK02991 358220006953 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 358220006954 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220006955 catalytic residue [active] 358220006956 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220006957 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 358220006958 Amidase; Region: Amidase; pfam01425 358220006959 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 358220006960 hydroxyglutarate oxidase; Provisional; Region: PRK11728 358220006961 Putative motility protein; Region: YjfB_motility; pfam14070 358220006962 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 358220006963 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220006964 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 358220006965 Uncharacterized conserved protein [Function unknown]; Region: COG1739 358220006966 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 358220006967 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 358220006968 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220006969 Coenzyme A binding pocket [chemical binding]; other site 358220006970 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220006971 putative DNA binding site [nucleotide binding]; other site 358220006972 putative Zn2+ binding site [ion binding]; other site 358220006973 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220006974 Coenzyme A binding pocket [chemical binding]; other site 358220006975 hypothetical protein; Provisional; Region: PRK01254 358220006976 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 358220006977 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 358220006978 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 358220006979 C-terminal FAT-like Four helix bundle domain, also called DUF3513, of CAS (Crk-Associated Substrate) scaffolding proteins; a protein interaction module; Region: FAT-like_CAS_C; cl13463 358220006980 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 358220006981 DNA-binding site [nucleotide binding]; DNA binding site 358220006982 RNA-binding motif; other site 358220006983 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 358220006984 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 358220006985 CoA-transferase family III; Region: CoA_transf_3; pfam02515 358220006986 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 358220006987 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 358220006988 putative active site [active] 358220006989 metal binding site [ion binding]; metal-binding site 358220006990 Bacterial protein of unknown function (DUF925); Region: DUF925; pfam06042 358220006991 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 358220006992 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220006993 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220006994 homodimer interface [polypeptide binding]; other site 358220006995 catalytic residue [active] 358220006996 excinuclease ABC subunit B; Provisional; Region: PRK05298 358220006997 Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes; Region: Motor_domain; cl00286 358220006998 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220006999 ATP-binding site [chemical binding]; other site 358220007000 ATP binding site [chemical binding]; other site 358220007001 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220007002 nucleotide binding region [chemical binding]; other site 358220007003 ATP-binding site [chemical binding]; other site 358220007004 Ultra-violet resistance protein B; Region: UvrB; pfam12344 358220007005 UvrB/uvrC motif; Region: UVR; pfam02151 358220007006 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 358220007007 Rrf2 family protein; Region: rrf2_super; TIGR00738 358220007008 cysteine desulfurase; Provisional; Region: PRK14012 358220007009 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 358220007010 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220007011 catalytic residue [active] 358220007012 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 358220007013 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 358220007014 trimerization site [polypeptide binding]; other site 358220007015 active site 358220007016 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 358220007017 co-chaperone HscB; Provisional; Region: hscB; PRK03578 358220007018 DnaJ domain; Region: DnaJ; pfam00226 358220007019 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 358220007020 chaperone protein HscA; Provisional; Region: hscA; PRK05183 358220007021 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 358220007022 nucleotide binding site [chemical binding]; other site 358220007023 putative NEF/HSP70 interaction site [polypeptide binding]; other site 358220007024 SBD interface [polypeptide binding]; other site 358220007025 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 358220007026 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220007027 catalytic loop [active] 358220007028 iron binding site [ion binding]; other site 358220007029 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 358220007030 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 358220007031 active site 358220007032 catalytic site [active] 358220007033 substrate binding site [chemical binding]; other site 358220007034 Histone deacetylase class IIa; Region: HDAC_classII_APAH; cd10001 358220007035 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 358220007036 active site 358220007037 Zn binding site [ion binding]; other site 358220007038 hydroxyglutarate oxidase; Provisional; Region: PRK11728 358220007039 Predicted dehydrogenase [General function prediction only]; Region: COG0579 358220007040 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 358220007041 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 358220007042 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 358220007043 quinone interaction residues [chemical binding]; other site 358220007044 active site 358220007045 catalytic residues [active] 358220007046 FMN binding site [chemical binding]; other site 358220007047 substrate binding site [chemical binding]; other site 358220007048 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 358220007049 tetramer (dimer of dimers) interface [polypeptide binding]; other site 358220007050 active site 358220007051 dimer interface [polypeptide binding]; other site 358220007052 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 358220007053 catalytic residues [active] 358220007054 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 358220007055 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 358220007056 active site 358220007057 Zn binding site [ion binding]; other site 358220007058 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 358220007059 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 358220007060 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 358220007061 homodimer interface [polypeptide binding]; other site 358220007062 NADP binding site [chemical binding]; other site 358220007063 substrate binding site [chemical binding]; other site 358220007064 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 358220007065 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220007066 active site 358220007067 phosphorylation site [posttranslational modification] 358220007068 intermolecular recognition site; other site 358220007069 dimerization interface [polypeptide binding]; other site 358220007070 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220007071 DNA binding residues [nucleotide binding] 358220007072 dimerization interface [polypeptide binding]; other site 358220007073 PAS domain S-box; Region: sensory_box; TIGR00229 358220007074 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007075 putative active site [active] 358220007076 heme pocket [chemical binding]; other site 358220007077 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220007078 dimer interface [polypeptide binding]; other site 358220007079 phosphorylation site [posttranslational modification] 358220007080 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220007081 ATP binding site [chemical binding]; other site 358220007082 Mg2+ binding site [ion binding]; other site 358220007083 G-X-G motif; other site 358220007084 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 358220007085 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 358220007086 dimer interface [polypeptide binding]; other site 358220007087 TPP-binding site [chemical binding]; other site 358220007088 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 358220007089 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 358220007090 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 358220007091 E3 interaction surface; other site 358220007092 lipoyl attachment site [posttranslational modification]; other site 358220007093 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 358220007094 E3 interaction surface; other site 358220007095 lipoyl attachment site [posttranslational modification]; other site 358220007096 e3 binding domain; Region: E3_binding; pfam02817 358220007097 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 358220007098 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 358220007099 E3 interaction surface; other site 358220007100 lipoyl attachment site [posttranslational modification]; other site 358220007101 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 358220007102 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 358220007103 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220007104 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 358220007105 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 358220007106 aspartate kinase; Validated; Region: PRK09181 358220007107 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 358220007108 nucleotide binding site [chemical binding]; other site 358220007109 substrate binding site [chemical binding]; other site 358220007110 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 358220007111 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 358220007112 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3395 358220007113 Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Region: RLP_NonPhot; cd08207 358220007114 Ribulose 1,5-bisphosphate carboxylase, large subunit [Carbohydrate transport and metabolism]; Region: RbcL; COG1850 358220007115 dimer interface [polypeptide binding]; other site 358220007116 active site 358220007117 catalytic residue [active] 358220007118 metal binding site [ion binding]; metal-binding site 358220007119 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 358220007120 dimer interface [polypeptide binding]; other site 358220007121 substrate binding site [chemical binding]; other site 358220007122 metal binding site [ion binding]; metal-binding site 358220007123 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220007124 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220007125 substrate binding pocket [chemical binding]; other site 358220007126 membrane-bound complex binding site; other site 358220007127 hinge residues; other site 358220007128 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 358220007129 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 358220007130 Walker A/P-loop; other site 358220007131 ATP binding site [chemical binding]; other site 358220007132 Q-loop/lid; other site 358220007133 ABC transporter signature motif; other site 358220007134 Walker B; other site 358220007135 D-loop; other site 358220007136 H-loop/switch region; other site 358220007137 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 358220007138 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220007139 dimer interface [polypeptide binding]; other site 358220007140 conserved gate region; other site 358220007141 putative PBP binding loops; other site 358220007142 ABC-ATPase subunit interface; other site 358220007143 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220007144 dimer interface [polypeptide binding]; other site 358220007145 conserved gate region; other site 358220007146 putative PBP binding loops; other site 358220007147 ABC-ATPase subunit interface; other site 358220007148 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 358220007149 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 358220007150 DNA binding site [nucleotide binding] 358220007151 Periplasmic sugar-binding domain of uncharacterized transport systems; Region: PBP1_uncharacterized_sugar_binding; cd06307 358220007152 putative ligand binding site [chemical binding]; other site 358220007153 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 358220007154 EamA-like transporter family; Region: EamA; pfam00892 358220007155 EamA-like transporter family; Region: EamA; pfam00892 358220007156 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220007157 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220007158 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 358220007159 putative dimerization interface [polypeptide binding]; other site 358220007160 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; cl17531 358220007161 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 358220007162 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 358220007163 GDP-mannose pyrophosphatase NudK; Provisional; Region: PRK15009 358220007164 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 358220007165 dimer interface [polypeptide binding]; other site 358220007166 ADP-ribose binding site [chemical binding]; other site 358220007167 active site 358220007168 nudix motif; other site 358220007169 metal binding site [ion binding]; metal-binding site 358220007170 Penicillin amidase; Region: Penicil_amidase; pfam01804 358220007171 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 358220007172 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 358220007173 active site 358220007174 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 358220007175 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 358220007176 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 358220007177 conserved cys residue [active] 358220007178 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220007179 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 358220007180 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220007181 S-adenosylmethionine binding site [chemical binding]; other site 358220007182 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 358220007183 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 358220007184 HAMP domain; Region: HAMP; pfam00672 358220007185 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007186 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220007187 putative active site [active] 358220007188 heme pocket [chemical binding]; other site 358220007189 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007190 putative active site [active] 358220007191 heme pocket [chemical binding]; other site 358220007192 PAS domain S-box; Region: sensory_box; TIGR00229 358220007193 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007194 putative active site [active] 358220007195 heme pocket [chemical binding]; other site 358220007196 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220007197 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220007198 metal binding site [ion binding]; metal-binding site 358220007199 active site 358220007200 I-site; other site 358220007201 EVE domain; Region: EVE; cl00728 358220007202 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 358220007203 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 358220007204 Uncharacterized protein conserved in bacteria (DUF2086); Region: DUF2086; pfam09859 358220007205 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 358220007206 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 358220007207 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220007208 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 358220007209 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 358220007210 DNA binding site [nucleotide binding] 358220007211 active site 358220007212 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 358220007213 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220007214 ATP binding site [chemical binding]; other site 358220007215 putative Mg++ binding site [ion binding]; other site 358220007216 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220007217 nucleotide binding region [chemical binding]; other site 358220007218 ATP-binding site [chemical binding]; other site 358220007219 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220007220 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220007221 DNA binding residues [nucleotide binding] 358220007222 dimerization interface [polypeptide binding]; other site 358220007223 Protein of unknown function (DUF3237); Region: DUF3237; pfam11578 358220007224 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220007225 Tannase and feruloyl esterase; Region: Tannase; pfam07519 358220007226 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 358220007227 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 358220007228 cyclase homology domain; Region: CHD; cd07302 358220007229 nucleotidyl binding site; other site 358220007230 metal binding site [ion binding]; metal-binding site 358220007231 dimer interface [polypeptide binding]; other site 358220007232 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 358220007233 NlpC/P60 family; Region: NLPC_P60; pfam00877 358220007234 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 358220007235 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 358220007236 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 358220007237 thymidine phosphorylase; Provisional; Region: PRK04350 358220007238 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 358220007239 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 358220007240 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 358220007241 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK07199 358220007242 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 358220007243 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220007244 active site 358220007245 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220007246 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220007247 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220007248 dimerization interface [polypeptide binding]; other site 358220007249 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220007250 metabolite-proton symporter; Region: 2A0106; TIGR00883 358220007251 putative substrate translocation pore; other site 358220007252 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 358220007253 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 358220007254 metal binding site [ion binding]; metal-binding site 358220007255 putative dimer interface [polypeptide binding]; other site 358220007256 glutaminase; Provisional; Region: PRK00971 358220007257 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 358220007258 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 358220007259 Isochorismatase family; Region: Isochorismatase; pfam00857 358220007260 catalytic triad [active] 358220007261 dimer interface [polypeptide binding]; other site 358220007262 conserved cis-peptide bond; other site 358220007263 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 358220007264 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 358220007265 Chromate transporter; Region: Chromate_transp; pfam02417 358220007266 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 358220007267 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220007268 acyl-activating enzyme (AAE) consensus motif; other site 358220007269 AMP binding site [chemical binding]; other site 358220007270 active site 358220007271 CoA binding site [chemical binding]; other site 358220007272 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 358220007273 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220007274 Coenzyme A binding pocket [chemical binding]; other site 358220007275 PAS fold; Region: PAS_3; pfam08447 358220007276 PAS domain S-box; Region: sensory_box; TIGR00229 358220007277 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007278 putative active site [active] 358220007279 heme pocket [chemical binding]; other site 358220007280 PAS domain S-box; Region: sensory_box; TIGR00229 358220007281 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007282 putative active site [active] 358220007283 heme pocket [chemical binding]; other site 358220007284 PAS domain S-box; Region: sensory_box; TIGR00229 358220007285 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007286 putative active site [active] 358220007287 heme pocket [chemical binding]; other site 358220007288 PAS fold; Region: PAS_3; pfam08447 358220007289 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220007290 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220007291 metal binding site [ion binding]; metal-binding site 358220007292 active site 358220007293 I-site; other site 358220007294 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220007295 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 358220007296 EamA-like transporter family; Region: EamA; pfam00892 358220007297 EamA-like transporter family; Region: EamA; pfam00892 358220007298 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 358220007299 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 358220007300 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 358220007301 DNA binding site [nucleotide binding] 358220007302 active site 358220007303 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 358220007304 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 358220007305 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220007306 AlkA N-terminal domain; Region: AlkA_N; pfam06029 358220007307 3-methyl-adenine DNA glycosylase II; Provisional; Region: PRK10308 358220007308 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 358220007309 minor groove reading motif; other site 358220007310 helix-hairpin-helix signature motif; other site 358220007311 active site 358220007312 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 358220007313 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 358220007314 active site 358220007315 substrate binding site [chemical binding]; other site 358220007316 metal binding site [ion binding]; metal-binding site 358220007317 Predicted amidohydrolase [General function prediction only]; Region: COG0388 358220007318 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 358220007319 active site 358220007320 catalytic triad [active] 358220007321 dimer interface [polypeptide binding]; other site 358220007322 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 358220007323 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 358220007324 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 358220007325 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 358220007326 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 358220007327 active site residue [active] 358220007328 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 358220007329 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220007330 S-adenosylmethionine binding site [chemical binding]; other site 358220007331 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 358220007332 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 358220007333 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 358220007334 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 358220007335 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 358220007336 Protein export membrane protein; Region: SecD_SecF; cl14618 358220007337 HlyD family secretion protein; Region: HlyD_2; pfam12700 358220007338 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220007339 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220007340 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220007341 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 358220007342 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220007343 DNA-binding site [nucleotide binding]; DNA binding site 358220007344 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 358220007345 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220007346 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_6; cd06340 358220007347 putative ligand binding site [chemical binding]; other site 358220007348 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220007349 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220007350 TM-ABC transporter signature motif; other site 358220007351 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220007352 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220007353 TM-ABC transporter signature motif; other site 358220007354 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220007355 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220007356 Walker A/P-loop; other site 358220007357 ATP binding site [chemical binding]; other site 358220007358 Q-loop/lid; other site 358220007359 ABC transporter signature motif; other site 358220007360 Walker B; other site 358220007361 D-loop; other site 358220007362 H-loop/switch region; other site 358220007363 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220007364 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220007365 Walker A/P-loop; other site 358220007366 ATP binding site [chemical binding]; other site 358220007367 Q-loop/lid; other site 358220007368 ABC transporter signature motif; other site 358220007369 Walker B; other site 358220007370 D-loop; other site 358220007371 H-loop/switch region; other site 358220007372 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220007373 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 358220007374 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 358220007375 substrate binding site [chemical binding]; other site 358220007376 ligand binding site [chemical binding]; other site 358220007377 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 358220007378 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 358220007379 substrate binding site [chemical binding]; other site 358220007380 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 358220007381 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 358220007382 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 358220007383 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 358220007384 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 358220007385 Isochorismatase family; Region: Isochorismatase; pfam00857 358220007386 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 358220007387 catalytic triad [active] 358220007388 conserved cis-peptide bond; other site 358220007389 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 358220007390 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 358220007391 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 358220007392 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 358220007393 tetramer interface [polypeptide binding]; other site 358220007394 active site 358220007395 Mg2+/Mn2+ binding site [ion binding]; other site 358220007396 methionine sulfoxide reductase A; Provisional; Region: PRK14054 358220007397 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 358220007398 putative DNA binding helix; other site 358220007399 metal binding site 2 [ion binding]; metal-binding site 358220007400 metal binding site 1 [ion binding]; metal-binding site 358220007401 dimer interface [polypeptide binding]; other site 358220007402 structural Zn2+ binding site [ion binding]; other site 358220007403 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 358220007404 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220007405 Walker A/P-loop; other site 358220007406 ATP binding site [chemical binding]; other site 358220007407 Q-loop/lid; other site 358220007408 ABC transporter signature motif; other site 358220007409 Walker B; other site 358220007410 D-loop; other site 358220007411 H-loop/switch region; other site 358220007412 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 358220007413 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 358220007414 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 358220007415 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 358220007416 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 358220007417 PAS fold; Region: PAS; pfam00989 358220007418 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007419 putative active site [active] 358220007420 heme pocket [chemical binding]; other site 358220007421 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007422 PAS fold; Region: PAS_3; pfam08447 358220007423 putative active site [active] 358220007424 heme pocket [chemical binding]; other site 358220007425 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007426 PAS fold; Region: PAS_3; pfam08447 358220007427 putative active site [active] 358220007428 heme pocket [chemical binding]; other site 358220007429 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220007430 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220007431 metal binding site [ion binding]; metal-binding site 358220007432 active site 358220007433 I-site; other site 358220007434 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220007435 ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: ModC; COG4148 358220007436 Walker A/P-loop; other site 358220007437 ATP binding site [chemical binding]; other site 358220007438 Q-loop/lid; other site 358220007439 ABC transporter signature motif; other site 358220007440 Walker B; other site 358220007441 D-loop; other site 358220007442 H-loop/switch region; other site 358220007443 TOBE domain; Region: TOBE; pfam03459 358220007444 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 358220007445 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220007446 putative PBP binding loops; other site 358220007447 dimer interface [polypeptide binding]; other site 358220007448 ABC-ATPase subunit interface; other site 358220007449 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 358220007450 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 358220007451 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 358220007452 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 358220007453 TOBE domain; Region: TOBE; cl01440 358220007454 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 358220007455 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220007456 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220007457 active site 358220007458 phosphorylation site [posttranslational modification] 358220007459 intermolecular recognition site; other site 358220007460 dimerization interface [polypeptide binding]; other site 358220007461 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 358220007462 DNA binding site [nucleotide binding] 358220007463 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 358220007464 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220007465 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220007466 dimer interface [polypeptide binding]; other site 358220007467 phosphorylation site [posttranslational modification] 358220007468 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220007469 ATP binding site [chemical binding]; other site 358220007470 Mg2+ binding site [ion binding]; other site 358220007471 G-X-G motif; other site 358220007472 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 358220007473 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220007474 Walker A/P-loop; other site 358220007475 ATP binding site [chemical binding]; other site 358220007476 Q-loop/lid; other site 358220007477 ABC transporter signature motif; other site 358220007478 Walker B; other site 358220007479 D-loop; other site 358220007480 H-loop/switch region; other site 358220007481 TOBE domain; Region: TOBE_2; pfam08402 358220007482 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 358220007483 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220007484 motif II; other site 358220007485 Predicted permeases [General function prediction only]; Region: COG0679 358220007486 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 358220007487 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 358220007488 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 358220007489 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220007490 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220007491 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 358220007492 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220007493 catalytic loop [active] 358220007494 iron binding site [ion binding]; other site 358220007495 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 358220007496 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220007497 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 358220007498 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 358220007499 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220007500 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220007501 AAA domain; Region: AAA_21; pfam13304 358220007502 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 358220007503 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 358220007504 phosphate binding site [ion binding]; other site 358220007505 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220007506 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220007507 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220007508 dimerization interface [polypeptide binding]; other site 358220007509 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 358220007510 metal-binding site 358220007511 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 358220007512 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 358220007513 E-class dimer interface [polypeptide binding]; other site 358220007514 P-class dimer interface [polypeptide binding]; other site 358220007515 active site 358220007516 Cu2+ binding site [ion binding]; other site 358220007517 Zn2+ binding site [ion binding]; other site 358220007518 Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]; Region: ChaC; COG3703 358220007519 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 358220007520 putative active site pocket [active] 358220007521 dimerization interface [polypeptide binding]; other site 358220007522 putative catalytic residue [active] 358220007523 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 358220007524 ligand binding site [chemical binding]; other site 358220007525 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220007526 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 358220007527 dimer interface [polypeptide binding]; other site 358220007528 active site 358220007529 metal binding site [ion binding]; metal-binding site 358220007530 glutathione binding site [chemical binding]; other site 358220007531 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220007532 CoenzymeA binding site [chemical binding]; other site 358220007533 subunit interaction site [polypeptide binding]; other site 358220007534 PHB binding site; other site 358220007535 Transcriptional regulators [Transcription]; Region: MarR; COG1846 358220007536 MarR family; Region: MarR_2; pfam12802 358220007537 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 358220007538 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220007539 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 358220007540 putative active site [active] 358220007541 putative catalytic site [active] 358220007542 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_3; cd13148 358220007543 putative efflux protein, MATE family; Region: matE; TIGR00797 358220007544 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 358220007545 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220007546 NAD(P) binding site [chemical binding]; other site 358220007547 active site 358220007548 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 358220007549 high affinity sulphate transporter 1; Region: sulP; TIGR00815 358220007550 Sulfate transporter family; Region: Sulfate_transp; pfam00916 358220007551 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 358220007552 Putative phosphatase (DUF442); Region: DUF442; cl17385 358220007553 Predicted transporter component [General function prediction only]; Region: COG2391 358220007554 Sulphur transport; Region: Sulf_transp; pfam04143 358220007555 Predicted transporter component [General function prediction only]; Region: COG2391 358220007556 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220007557 dimerization interface [polypeptide binding]; other site 358220007558 putative DNA binding site [nucleotide binding]; other site 358220007559 putative Zn2+ binding site [ion binding]; other site 358220007560 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 358220007561 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 358220007562 active site residue [active] 358220007563 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 358220007564 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 358220007565 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 358220007566 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220007567 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220007568 dimer interface [polypeptide binding]; other site 358220007569 phosphorylation site [posttranslational modification] 358220007570 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220007571 ATP binding site [chemical binding]; other site 358220007572 Mg2+ binding site [ion binding]; other site 358220007573 G-X-G motif; other site 358220007574 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220007575 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220007576 active site 358220007577 phosphorylation site [posttranslational modification] 358220007578 intermolecular recognition site; other site 358220007579 dimerization interface [polypeptide binding]; other site 358220007580 Response regulator receiver domain; Region: Response_reg; pfam00072 358220007581 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220007582 active site 358220007583 phosphorylation site [posttranslational modification] 358220007584 intermolecular recognition site; other site 358220007585 dimerization interface [polypeptide binding]; other site 358220007586 Hpt domain; Region: Hpt; pfam01627 358220007587 putative binding surface; other site 358220007588 active site 358220007589 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 358220007590 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220007591 active site 358220007592 phosphorylation site [posttranslational modification] 358220007593 intermolecular recognition site; other site 358220007594 dimerization interface [polypeptide binding]; other site 358220007595 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220007596 Zn2+ binding site [ion binding]; other site 358220007597 Mg2+ binding site [ion binding]; other site 358220007598 biotin synthase; Region: bioB; TIGR00433 358220007599 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220007600 FeS/SAM binding site; other site 358220007601 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 358220007602 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 358220007603 dimer interface [polypeptide binding]; other site 358220007604 substrate binding site [chemical binding]; other site 358220007605 metal binding site [ion binding]; metal-binding site 358220007606 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 358220007607 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 358220007608 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 358220007609 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 358220007610 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 358220007611 carboxyltransferase (CT) interaction site; other site 358220007612 biotinylation site [posttranslational modification]; other site 358220007613 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 358220007614 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 358220007615 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 358220007616 membrane ATPase/protein kinase; Provisional; Region: PRK09435 358220007617 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 358220007618 Walker A; other site 358220007619 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 358220007620 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 358220007621 active site 358220007622 substrate binding site [chemical binding]; other site 358220007623 coenzyme B12 binding site [chemical binding]; other site 358220007624 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 358220007625 B12 binding site [chemical binding]; other site 358220007626 cobalt ligand [ion binding]; other site 358220007627 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220007628 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220007629 DNA-binding site [nucleotide binding]; DNA binding site 358220007630 FCD domain; Region: FCD; pfam07729 358220007631 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 358220007632 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 358220007633 acyl-activating enzyme (AAE) consensus motif; other site 358220007634 putative AMP binding site [chemical binding]; other site 358220007635 putative active site [active] 358220007636 putative CoA binding site [chemical binding]; other site 358220007637 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 358220007638 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 358220007639 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220007640 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 358220007641 putative DNA binding site [nucleotide binding]; other site 358220007642 putative Zn2+ binding site [ion binding]; other site 358220007643 AsnC family; Region: AsnC_trans_reg; pfam01037 358220007644 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 358220007645 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 358220007646 putative acyl-acceptor binding pocket; other site 358220007647 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 358220007648 Fatty acid desaturase; Region: FA_desaturase; pfam00487 358220007649 Di-iron ligands [ion binding]; other site 358220007650 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 358220007651 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 358220007652 oligomerization interface [polypeptide binding]; other site 358220007653 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 358220007654 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 358220007655 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 358220007656 active site 358220007657 Phage-related protein [Function unknown]; Region: COG4695 358220007658 Phage portal protein; Region: Phage_portal; pfam04860 358220007659 Caudovirus prohead protease; Region: Peptidase_U35; pfam04586 358220007660 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 358220007661 Phage capsid family; Region: Phage_capsid; pfam05065 358220007662 AAA domain; Region: AAA_25; pfam13481 358220007663 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220007664 ATP binding site [chemical binding]; other site 358220007665 Walker B motif; other site 358220007666 CHC2 zinc finger; Region: zf-CHC2; cl17510 358220007667 Helix-turn-helix domain; Region: HTH_17; cl17695 358220007668 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 358220007669 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220007670 active site 358220007671 DNA binding site [nucleotide binding] 358220007672 Int/Topo IB signature motif; other site 358220007673 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 358220007674 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 358220007675 FMN binding site [chemical binding]; other site 358220007676 active site 358220007677 catalytic residues [active] 358220007678 substrate binding site [chemical binding]; other site 358220007679 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 358220007680 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 358220007681 CHASE domain; Region: CHASE; pfam03924 358220007682 PAS fold; Region: PAS_4; pfam08448 358220007683 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220007684 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220007685 metal binding site [ion binding]; metal-binding site 358220007686 active site 358220007687 I-site; other site 358220007688 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220007689 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 358220007690 synthetase active site [active] 358220007691 NTP binding site [chemical binding]; other site 358220007692 metal binding site [ion binding]; metal-binding site 358220007693 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 358220007694 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 358220007695 ferredoxin; Provisional; Region: PRK08764 358220007696 Putative Fe-S cluster; Region: FeS; cl17515 358220007697 4Fe-4S binding domain; Region: Fer4; pfam00037 358220007698 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220007699 dimerization interface [polypeptide binding]; other site 358220007700 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220007701 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220007702 dimer interface [polypeptide binding]; other site 358220007703 putative CheW interface [polypeptide binding]; other site 358220007704 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 358220007705 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220007706 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220007707 homodimer interface [polypeptide binding]; other site 358220007708 catalytic residue [active] 358220007709 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 358220007710 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 358220007711 active site 358220007712 substrate binding site [chemical binding]; other site 358220007713 trimer interface [polypeptide binding]; other site 358220007714 CoA binding site [chemical binding]; other site 358220007715 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 358220007716 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220007717 Walker A motif; other site 358220007718 ATP binding site [chemical binding]; other site 358220007719 Walker B motif; other site 358220007720 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 358220007721 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 358220007722 metal binding site [ion binding]; metal-binding site 358220007723 dimer interface [polypeptide binding]; other site 358220007724 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 358220007725 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220007726 S-adenosylmethionine binding site [chemical binding]; other site 358220007727 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 358220007728 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 358220007729 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 358220007730 ABC transporter; Region: ABC_tran_2; pfam12848 358220007731 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 358220007732 acetyacetyl-CoA reductase; Provisional; Region: PRK12938 358220007733 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 358220007734 NAD(P) binding site [chemical binding]; other site 358220007735 homotetramer interface [polypeptide binding]; other site 358220007736 homodimer interface [polypeptide binding]; other site 358220007737 active site 358220007738 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220007739 putative transposase OrfB; Reviewed; Region: PHA02517 358220007740 Integrase core domain; Region: rve; pfam00665 358220007741 Integrase core domain; Region: rve_3; pfam13683 358220007742 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220007743 Homeodomain-like domain; Region: HTH_23; cl17451 358220007744 putative acyltransferase; Provisional; Region: PRK05790 358220007745 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220007746 dimer interface [polypeptide binding]; other site 358220007747 active site 358220007748 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 358220007749 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 358220007750 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 358220007751 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 358220007752 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 358220007753 maleylacetoacetate isomerase; Region: maiA; TIGR01262 358220007754 C-terminal domain interface [polypeptide binding]; other site 358220007755 GSH binding site (G-site) [chemical binding]; other site 358220007756 putative dimer interface [polypeptide binding]; other site 358220007757 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 358220007758 N-terminal domain interface [polypeptide binding]; other site 358220007759 dimer interface [polypeptide binding]; other site 358220007760 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 358220007761 MarR family; Region: MarR_2; cl17246 358220007762 Transcriptional regulators [Transcription]; Region: MarR; COG1846 358220007763 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 358220007764 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 358220007765 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 358220007766 nudix motif; other site 358220007767 Domain of unknown function (DUF1737); Region: DUF1737; pfam08410 358220007768 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 358220007769 Transglycosylase; Region: Transgly; pfam00912 358220007770 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 358220007771 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 358220007772 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 358220007773 nucleotide binding pocket [chemical binding]; other site 358220007774 K-X-D-G motif; other site 358220007775 catalytic site [active] 358220007776 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 358220007777 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 358220007778 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo...; Region: BRCT; cd00027 358220007779 Dimer interface [polypeptide binding]; other site 358220007780 BRCT sequence motif; other site 358220007781 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cl12038 358220007782 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 358220007783 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 358220007784 Walker A/P-loop; other site 358220007785 ATP binding site [chemical binding]; other site 358220007786 Q-loop/lid; other site 358220007787 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 358220007788 ABC transporter signature motif; other site 358220007789 Walker B; other site 358220007790 D-loop; other site 358220007791 H-loop/switch region; other site 358220007792 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220007793 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220007794 metal binding site [ion binding]; metal-binding site 358220007795 active site 358220007796 I-site; other site 358220007797 This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases; Region: CHASE; smart01079 358220007798 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007799 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220007800 putative active site [active] 358220007801 heme pocket [chemical binding]; other site 358220007802 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007803 putative active site [active] 358220007804 heme pocket [chemical binding]; other site 358220007805 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220007806 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220007807 metal binding site [ion binding]; metal-binding site 358220007808 active site 358220007809 I-site; other site 358220007810 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220007811 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 358220007812 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220007813 sequence-specific DNA binding site [nucleotide binding]; other site 358220007814 salt bridge; other site 358220007815 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 358220007816 Domain of unknown function (DUF955); Region: DUF955; pfam06114 358220007817 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 358220007818 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 358220007819 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 358220007820 Subgroup of Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS)...; Region: Ec2MCS_like_1; cd06117 358220007821 dimer interface [polypeptide binding]; other site 358220007822 active site 358220007823 citrylCoA binding site [chemical binding]; other site 358220007824 oxalacetate/citrate binding site [chemical binding]; other site 358220007825 coenzyme A binding site [chemical binding]; other site 358220007826 catalytic triad [active] 358220007827 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 358220007828 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 358220007829 substrate binding site [chemical binding]; other site 358220007830 ligand binding site [chemical binding]; other site 358220007831 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 358220007832 substrate binding site [chemical binding]; other site 358220007833 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 358220007834 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 358220007835 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 358220007836 tetramer interface [polypeptide binding]; other site 358220007837 active site 358220007838 Mg2+/Mn2+ binding site [ion binding]; other site 358220007839 PAS domain; Region: PAS_9; pfam13426 358220007840 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007841 putative active site [active] 358220007842 heme pocket [chemical binding]; other site 358220007843 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220007844 GAF domain; Region: GAF_3; pfam13492 358220007845 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220007846 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220007847 metal binding site [ion binding]; metal-binding site 358220007848 active site 358220007849 I-site; other site 358220007850 Predicted integral membrane protein [Function unknown]; Region: COG5615 358220007851 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 358220007852 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 358220007853 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 358220007854 Walker A/P-loop; other site 358220007855 ATP binding site [chemical binding]; other site 358220007856 Q-loop/lid; other site 358220007857 ABC transporter signature motif; other site 358220007858 Walker B; other site 358220007859 D-loop; other site 358220007860 H-loop/switch region; other site 358220007861 EthD domain; Region: EthD; cl17553 358220007862 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220007863 non-specific DNA binding site [nucleotide binding]; other site 358220007864 salt bridge; other site 358220007865 sequence-specific DNA binding site [nucleotide binding]; other site 358220007866 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220007867 6-phosphogluconolactonase; Provisional; Region: PRK11028 358220007868 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220007869 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 358220007870 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH); Region: KDGDH; cd00951 358220007871 putative active site [active] 358220007872 catalytic residue [active] 358220007873 SnoaL-like domain; Region: SnoaL_2; pfam12680 358220007874 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 358220007875 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 358220007876 putative ligand binding site [chemical binding]; other site 358220007877 NAD binding site [chemical binding]; other site 358220007878 catalytic site [active] 358220007879 glutamate carboxypeptidase; Reviewed; Region: PRK06133 358220007880 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 358220007881 metal binding site [ion binding]; metal-binding site 358220007882 dimer interface [polypeptide binding]; other site 358220007883 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220007884 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220007885 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 358220007886 substrate binding pocket [chemical binding]; other site 358220007887 dimerization interface [polypeptide binding]; other site 358220007888 SnoaL-like domain; Region: SnoaL_2; pfam12680 358220007889 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 358220007890 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220007891 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 358220007892 putative dimerization interface [polypeptide binding]; other site 358220007893 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 358220007894 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 358220007895 THF binding site; other site 358220007896 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 358220007897 substrate binding site [chemical binding]; other site 358220007898 THF binding site; other site 358220007899 zinc-binding site [ion binding]; other site 358220007900 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 358220007901 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 358220007902 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 358220007903 Transcriptional regulators [Transcription]; Region: MarR; COG1846 358220007904 MarR family; Region: MarR; pfam01047 358220007905 MarR family; Region: MarR_2; cl17246 358220007906 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 358220007907 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 358220007908 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220007909 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220007910 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 358220007911 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220007912 putative substrate translocation pore; other site 358220007913 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220007914 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 358220007915 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007916 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 358220007917 putative active site [active] 358220007918 heme pocket [chemical binding]; other site 358220007919 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220007920 dimer interface [polypeptide binding]; other site 358220007921 phosphorylation site [posttranslational modification] 358220007922 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220007923 ATP binding site [chemical binding]; other site 358220007924 Mg2+ binding site [ion binding]; other site 358220007925 G-X-G motif; other site 358220007926 EF-hand domain pair; Region: EF_hand_6; pfam13833 358220007927 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 358220007928 Ca2+ binding site [ion binding]; other site 358220007929 EF-hand domain pair; Region: EF_hand_5; pfam13499 358220007930 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 358220007931 Ca2+ binding site [ion binding]; other site 358220007932 Putative thioesterase (yiiD_Cterm); Region: YiiD_Cterm; pfam09500 358220007933 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 358220007934 nudix motif; other site 358220007935 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220007936 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220007937 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220007938 dimerization interface [polypeptide binding]; other site 358220007939 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 358220007940 MarR family; Region: MarR; pfam01047 358220007941 salicylate hydroxylase; Provisional; Region: PRK08163 358220007942 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220007943 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3435 358220007944 Cupin domain; Region: Cupin_2; pfam07883 358220007945 Cupin domain; Region: Cupin_2; cl17218 358220007946 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 358220007947 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 358220007948 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 358220007949 C-terminal domain interface [polypeptide binding]; other site 358220007950 GSH binding site (G-site) [chemical binding]; other site 358220007951 putative dimer interface [polypeptide binding]; other site 358220007952 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 358220007953 dimer interface [polypeptide binding]; other site 358220007954 N-terminal domain interface [polypeptide binding]; other site 358220007955 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 358220007956 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220007957 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 358220007958 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 358220007959 tetrameric interface [polypeptide binding]; other site 358220007960 NAD binding site [chemical binding]; other site 358220007961 catalytic residues [active] 358220007962 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 358220007963 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220007964 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220007965 active site 358220007966 Protein of unknown function, DUF488; Region: DUF488; cl01246 358220007967 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 358220007968 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 358220007969 Response regulator receiver domain; Region: Response_reg; pfam00072 358220007970 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220007971 active site 358220007972 phosphorylation site [posttranslational modification] 358220007973 intermolecular recognition site; other site 358220007974 dimerization interface [polypeptide binding]; other site 358220007975 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220007976 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 358220007977 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220007978 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 358220007979 putative active site [active] 358220007980 heme pocket [chemical binding]; other site 358220007981 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007982 putative active site [active] 358220007983 heme pocket [chemical binding]; other site 358220007984 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220007985 GAF domain; Region: GAF; pfam01590 358220007986 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220007987 metal binding site [ion binding]; metal-binding site 358220007988 active site 358220007989 I-site; other site 358220007990 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220007991 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220007992 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220007993 active site 358220007994 phosphorylation site [posttranslational modification] 358220007995 intermolecular recognition site; other site 358220007996 dimerization interface [polypeptide binding]; other site 358220007997 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220007998 PAS domain; Region: PAS_9; pfam13426 358220007999 putative active site [active] 358220008000 heme pocket [chemical binding]; other site 358220008001 PAS domain S-box; Region: sensory_box; TIGR00229 358220008002 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220008003 putative active site [active] 358220008004 heme pocket [chemical binding]; other site 358220008005 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 358220008006 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220008007 putative active site [active] 358220008008 heme pocket [chemical binding]; other site 358220008009 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220008010 dimer interface [polypeptide binding]; other site 358220008011 phosphorylation site [posttranslational modification] 358220008012 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220008013 ATP binding site [chemical binding]; other site 358220008014 Mg2+ binding site [ion binding]; other site 358220008015 G-X-G motif; other site 358220008016 isocitrate dehydrogenase; Validated; Region: PRK07362 358220008017 isocitrate dehydrogenase; Reviewed; Region: PRK07006 358220008018 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 358220008019 superoxide dismutase; Provisional; Region: PRK10543 358220008020 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 358220008021 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 358220008022 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 358220008023 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 358220008024 generic binding surface II; other site 358220008025 generic binding surface I; other site 358220008026 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 358220008027 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 358220008028 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 358220008029 tetraacyldisaccharide 4'-kinase; Provisional; Region: PRK01906 358220008030 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 358220008031 Uncharacterized conserved protein [Function unknown]; Region: COG2835 358220008032 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 358220008033 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 358220008034 Ligand binding site; other site 358220008035 oligomer interface; other site 358220008036 adenylate kinase; Reviewed; Region: adk; PRK00279 358220008037 Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for...; Region: ADK; cd01428 358220008038 AMP-binding site [chemical binding]; other site 358220008039 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 358220008040 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 358220008041 active site 358220008042 homotetramer interface [polypeptide binding]; other site 358220008043 homodimer interface [polypeptide binding]; other site 358220008044 LexA repressor; Validated; Region: PRK00215 358220008045 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 358220008046 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 358220008047 Catalytic site [active] 358220008048 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 358220008049 Putative D-3-Phosphoglycerate Dehydrogenases; Region: PGDH_like_1; cd12169 358220008050 dimerization interface [polypeptide binding]; other site 358220008051 NAD binding site [chemical binding]; other site 358220008052 ligand binding site [chemical binding]; other site 358220008053 catalytic site [active] 358220008054 putative transposase OrfB; Reviewed; Region: PHA02517 358220008055 Integrase core domain; Region: rve; pfam00665 358220008056 Integrase core domain; Region: rve_3; pfam13683 358220008057 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220008058 Homeodomain-like domain; Region: HTH_23; cl17451 358220008059 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220008060 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 358220008061 dimerization interface [polypeptide binding]; other site 358220008062 ligand binding site [chemical binding]; other site 358220008063 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 358220008064 multifunctional aminopeptidase A; Provisional; Region: PRK00913 358220008065 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 358220008066 interface (dimer of trimers) [polypeptide binding]; other site 358220008067 Substrate-binding/catalytic site; other site 358220008068 Zn-binding sites [ion binding]; other site 358220008069 Predicted permeases [General function prediction only]; Region: COG0795 358220008070 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 358220008071 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 358220008072 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 358220008073 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 358220008074 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 358220008075 putative active site [active] 358220008076 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 358220008077 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220008078 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 358220008079 substrate binding site [chemical binding]; other site 358220008080 dimerization interface [polypeptide binding]; other site 358220008081 methionine aminotransferase; Validated; Region: PRK09082 358220008082 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220008083 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220008084 homodimer interface [polypeptide binding]; other site 358220008085 catalytic residue [active] 358220008086 EamA-like transporter family; Region: EamA; pfam00892 358220008087 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 358220008088 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 358220008089 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220008090 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 358220008091 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 358220008092 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 358220008093 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 358220008094 Ligand Binding Site [chemical binding]; other site 358220008095 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 358220008096 GAF domain; Region: GAF_3; pfam13492 358220008097 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220008098 dimer interface [polypeptide binding]; other site 358220008099 phosphorylation site [posttranslational modification] 358220008100 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220008101 ATP binding site [chemical binding]; other site 358220008102 Mg2+ binding site [ion binding]; other site 358220008103 G-X-G motif; other site 358220008104 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 358220008105 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220008106 active site 358220008107 phosphorylation site [posttranslational modification] 358220008108 intermolecular recognition site; other site 358220008109 dimerization interface [polypeptide binding]; other site 358220008110 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220008111 DNA binding site [nucleotide binding] 358220008112 HTH domain; Region: HTH_11; pfam08279 358220008113 Predicted transcriptional regulator [Transcription]; Region: COG2378 358220008114 WYL domain; Region: WYL; pfam13280 358220008115 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 358220008116 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220008117 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 358220008118 N-terminal domain interface [polypeptide binding]; other site 358220008119 ribonuclease G; Provisional; Region: PRK11712 358220008120 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 358220008121 homodimer interface [polypeptide binding]; other site 358220008122 oligonucleotide binding site [chemical binding]; other site 358220008123 Maf-like protein; Region: Maf; pfam02545 358220008124 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 358220008125 active site 358220008126 dimer interface [polypeptide binding]; other site 358220008127 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 358220008128 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 358220008129 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 358220008130 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 358220008131 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 358220008132 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 358220008133 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 358220008134 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 358220008135 hypothetical protein; Validated; Region: PRK00110 358220008136 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 358220008137 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 358220008138 Uncharacterized conserved protein [Function unknown]; Region: COG4278 358220008139 enoyl-CoA hydratase; Provisional; Region: PRK06142 358220008140 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220008141 substrate binding site [chemical binding]; other site 358220008142 oxyanion hole (OAH) forming residues; other site 358220008143 trimer interface [polypeptide binding]; other site 358220008144 M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily; Region: M20_Acy1L2_AbgB; cd05673 358220008145 amidohydrolase; Region: amidohydrolases; TIGR01891 358220008146 putative metal binding site [ion binding]; other site 358220008147 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220008148 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220008149 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220008150 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220008151 dimerization interface [polypeptide binding]; other site 358220008152 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 358220008153 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 358220008154 tetramer interface [polypeptide binding]; other site 358220008155 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220008156 catalytic residue [active] 358220008157 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220008158 active site 358220008159 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 358220008160 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 358220008161 putative ligand binding site [chemical binding]; other site 358220008162 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 358220008163 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 358220008164 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 358220008165 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 358220008166 Walker A/P-loop; other site 358220008167 ATP binding site [chemical binding]; other site 358220008168 Q-loop/lid; other site 358220008169 ABC transporter signature motif; other site 358220008170 Walker B; other site 358220008171 D-loop; other site 358220008172 H-loop/switch region; other site 358220008173 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 358220008174 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 358220008175 TM-ABC transporter signature motif; other site 358220008176 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220008177 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 358220008178 TM-ABC transporter signature motif; other site 358220008179 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220008180 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 358220008181 cytosine deaminase; Validated; Region: PRK07572 358220008182 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi; Region: Bact_CD; cd01293 358220008183 active site 358220008184 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 358220008185 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 358220008186 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 358220008187 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 358220008188 Walker A/P-loop; other site 358220008189 ATP binding site [chemical binding]; other site 358220008190 Q-loop/lid; other site 358220008191 ABC transporter signature motif; other site 358220008192 Walker B; other site 358220008193 D-loop; other site 358220008194 H-loop/switch region; other site 358220008195 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 358220008196 Walker A/P-loop; other site 358220008197 ATP binding site [chemical binding]; other site 358220008198 Q-loop/lid; other site 358220008199 ABC transporter signature motif; other site 358220008200 Walker B; other site 358220008201 D-loop; other site 358220008202 H-loop/switch region; other site 358220008203 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 358220008204 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 358220008205 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 358220008206 HlyD family secretion protein; Region: HlyD; pfam00529 358220008207 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220008208 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220008209 Protein of unknown function (DUF1569); Region: DUF1569; pfam07606 358220008210 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220008211 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220008212 metal binding site [ion binding]; metal-binding site 358220008213 active site 358220008214 I-site; other site 358220008215 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 358220008216 HSP70 interaction site [polypeptide binding]; other site 358220008217 hypothetical protein; Provisional; Region: PRK12378 358220008218 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 358220008219 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 358220008220 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 358220008221 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 358220008222 active site 358220008223 ATP binding site [chemical binding]; other site 358220008224 substrate binding site [chemical binding]; other site 358220008225 activation loop (A-loop); other site 358220008226 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220008227 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220008228 ligand binding site [chemical binding]; other site 358220008229 flexible hinge region; other site 358220008230 hypothetical protein; Provisional; Region: PRK05939 358220008231 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 358220008232 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220008233 catalytic residue [active] 358220008234 exonuclease I; Provisional; Region: sbcB; PRK11779 358220008235 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 358220008236 active site 358220008237 catalytic site [active] 358220008238 substrate binding site [chemical binding]; other site 358220008239 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 358220008240 Transglycosylase SLT domain; Region: SLT_2; pfam13406 358220008241 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 358220008242 N-acetyl-D-glucosamine binding site [chemical binding]; other site 358220008243 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 358220008244 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4430 358220008245 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 358220008246 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 358220008247 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 358220008248 putative active site [active] 358220008249 putative PHP Thumb interface [polypeptide binding]; other site 358220008250 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 358220008251 generic binding surface II; other site 358220008252 generic binding surface I; other site 358220008253 Y-family of DNA polymerases; Region: PolY; cl12025 358220008254 DNA binding site [nucleotide binding] 358220008255 Uncharacterized conserved protein [Function unknown]; Region: COG4544 358220008256 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220008257 Zn2+ binding site [ion binding]; other site 358220008258 Mg2+ binding site [ion binding]; other site 358220008259 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 358220008260 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 358220008261 PAS domain; Region: PAS_9; pfam13426 358220008262 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220008263 putative active site [active] 358220008264 heme pocket [chemical binding]; other site 358220008265 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220008266 DNA binding residues [nucleotide binding] 358220008267 dimerization interface [polypeptide binding]; other site 358220008268 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 358220008269 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 358220008270 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 358220008271 dimer interface [polypeptide binding]; other site 358220008272 active site 358220008273 heme binding site [chemical binding]; other site 358220008274 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 358220008275 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 358220008276 Strictosidine synthase; Region: Str_synth; pfam03088 358220008277 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 358220008278 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 358220008279 active site 358220008280 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220008281 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220008282 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220008283 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 358220008284 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 358220008285 ligand binding site [chemical binding]; other site 358220008286 NAD binding site [chemical binding]; other site 358220008287 dimerization interface [polypeptide binding]; other site 358220008288 catalytic site [active] 358220008289 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 358220008290 hypothetical protein; Validated; Region: PRK06201 358220008291 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220008292 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 358220008293 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 358220008294 active site 358220008295 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220008296 Transcriptional regulator [Transcription]; Region: IclR; COG1414 358220008297 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 358220008298 Bacterial transcriptional regulator; Region: IclR; pfam01614 358220008299 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 358220008300 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 358220008301 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 358220008302 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220008303 PAS domain; Region: PAS_9; pfam13426 358220008304 putative active site [active] 358220008305 heme pocket [chemical binding]; other site 358220008306 PAS domain S-box; Region: sensory_box; TIGR00229 358220008307 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220008308 putative active site [active] 358220008309 heme pocket [chemical binding]; other site 358220008310 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220008311 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220008312 metal binding site [ion binding]; metal-binding site 358220008313 active site 358220008314 I-site; other site 358220008315 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220008316 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220008317 Integrase core domain; Region: rve; pfam00665 358220008318 Integrase core domain; Region: rve_3; cl15866 358220008319 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220008320 Helix-turn-helix domain; Region: HTH_38; pfam13936 358220008321 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 358220008322 active site 358220008323 short chain dehydrogenase; Provisional; Region: PRK06949 358220008324 classical (c) SDRs; Region: SDR_c; cd05233 358220008325 NAD(P) binding site [chemical binding]; other site 358220008326 active site 358220008327 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 358220008328 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 358220008329 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 358220008330 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220008331 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220008332 dimerization interface [polypeptide binding]; other site 358220008333 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220008334 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220008335 dimer interface [polypeptide binding]; other site 358220008336 putative CheW interface [polypeptide binding]; other site 358220008337 5-oxoprolinase; Region: PLN02666 358220008338 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 358220008339 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 358220008340 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 358220008341 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 358220008342 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 358220008343 DctM-like transporters; Region: DctM; pfam06808 358220008344 DEAD-like helicases superfamily; Region: DEXDc; smart00487 358220008345 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220008346 ATP binding site [chemical binding]; other site 358220008347 putative Mg++ binding site [ion binding]; other site 358220008348 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220008349 nucleotide binding region [chemical binding]; other site 358220008350 ATP-binding site [chemical binding]; other site 358220008351 Helicase associated domain (HA2); Region: HA2; pfam04408 358220008352 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 358220008353 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 358220008354 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 358220008355 Beta-lactamase; Region: Beta-lactamase; pfam00144 358220008356 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220008357 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 358220008358 Walker A motif; other site 358220008359 ATP binding site [chemical binding]; other site 358220008360 Walker B motif; other site 358220008361 Peptidase family M41; Region: Peptidase_M41; pfam01434 358220008362 N-acetylglutamate synthase; Validated; Region: PRK05279 358220008363 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 358220008364 putative feedback inhibition sensing region; other site 358220008365 putative nucleotide binding site [chemical binding]; other site 358220008366 putative substrate binding site [chemical binding]; other site 358220008367 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220008368 Coenzyme A binding pocket [chemical binding]; other site 358220008369 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 358220008370 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220008371 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220008372 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220008373 dimerization interface [polypeptide binding]; other site 358220008374 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 358220008375 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 358220008376 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220008377 Zn2+ binding site [ion binding]; other site 358220008378 Mg2+ binding site [ion binding]; other site 358220008379 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220008380 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 358220008381 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 358220008382 active site residue [active] 358220008383 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 358220008384 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220008385 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 358220008386 putative N-terminal domain interface [polypeptide binding]; other site 358220008387 putative dimer interface [polypeptide binding]; other site 358220008388 putative substrate binding pocket (H-site) [chemical binding]; other site 358220008389 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 358220008390 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 358220008391 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 358220008392 Walker A/P-loop; other site 358220008393 ATP binding site [chemical binding]; other site 358220008394 Q-loop/lid; other site 358220008395 ABC transporter signature motif; other site 358220008396 Walker B; other site 358220008397 D-loop; other site 358220008398 H-loop/switch region; other site 358220008399 TOBE-like domain; Region: TOBE_3; pfam12857 358220008400 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220008401 dimer interface [polypeptide binding]; other site 358220008402 conserved gate region; other site 358220008403 putative PBP binding loops; other site 358220008404 ABC-ATPase subunit interface; other site 358220008405 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 358220008406 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220008407 dimer interface [polypeptide binding]; other site 358220008408 conserved gate region; other site 358220008409 putative PBP binding loops; other site 358220008410 ABC-ATPase subunit interface; other site 358220008411 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 358220008412 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 358220008413 Serine hydrolase; Region: Ser_hydrolase; pfam06821 358220008414 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220008415 RNA polymerase sigma factor; Provisional; Region: PRK12513 358220008416 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220008417 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220008418 DNA binding residues [nucleotide binding] 358220008419 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 358220008420 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 358220008421 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 358220008422 HDOD domain; Region: HDOD; pfam08668 358220008423 LysR family transcriptional regulator; Provisional; Region: PRK14997 358220008424 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220008425 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 358220008426 putative effector binding pocket; other site 358220008427 putative dimerization interface [polypeptide binding]; other site 358220008428 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 358220008429 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 358220008430 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 358220008431 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220008432 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220008433 metal binding site [ion binding]; metal-binding site 358220008434 active site 358220008435 I-site; other site 358220008436 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220008437 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 358220008438 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 358220008439 Protein of unknown function DUF72; Region: DUF72; pfam01904 358220008440 SnoaL-like domain; Region: SnoaL_3; pfam13474 358220008441 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220008442 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220008443 metal binding site [ion binding]; metal-binding site 358220008444 active site 358220008445 I-site; other site 358220008446 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 358220008447 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 358220008448 DNA binding site [nucleotide binding] 358220008449 active site 358220008450 hypothetical protein; Provisional; Region: PRK06194 358220008451 classical (c) SDRs; Region: SDR_c; cd05233 358220008452 NAD(P) binding site [chemical binding]; other site 358220008453 active site 358220008454 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220008455 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 358220008456 C-terminal domain interface [polypeptide binding]; other site 358220008457 GSH binding site (G-site) [chemical binding]; other site 358220008458 dimer interface [polypeptide binding]; other site 358220008459 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 358220008460 N-terminal domain interface [polypeptide binding]; other site 358220008461 dimer interface [polypeptide binding]; other site 358220008462 substrate binding pocket (H-site) [chemical binding]; other site 358220008463 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220008464 active site 358220008465 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220008466 Coenzyme A binding pocket [chemical binding]; other site 358220008467 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 358220008468 Prostaglandin dehydrogenases; Region: PGDH; cd05288 358220008469 NAD(P) binding site [chemical binding]; other site 358220008470 substrate binding site [chemical binding]; other site 358220008471 dimer interface [polypeptide binding]; other site 358220008472 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220008473 CoenzymeA binding site [chemical binding]; other site 358220008474 subunit interaction site [polypeptide binding]; other site 358220008475 PHB binding site; other site 358220008476 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 358220008477 classical (c) SDRs; Region: SDR_c; cd05233 358220008478 NAD(P) binding site [chemical binding]; other site 358220008479 active site 358220008480 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 358220008481 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220008482 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220008483 active site 358220008484 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 358220008485 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220008486 CoenzymeA binding site [chemical binding]; other site 358220008487 subunit interaction site [polypeptide binding]; other site 358220008488 PHB binding site; other site 358220008489 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 358220008490 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220008491 dimer interface [polypeptide binding]; other site 358220008492 active site 358220008493 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220008494 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 358220008495 substrate binding site [chemical binding]; other site 358220008496 oxyanion hole (OAH) forming residues; other site 358220008497 trimer interface [polypeptide binding]; other site 358220008498 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220008499 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220008500 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220008501 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220008502 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220008503 Walker A/P-loop; other site 358220008504 ATP binding site [chemical binding]; other site 358220008505 Q-loop/lid; other site 358220008506 ABC transporter signature motif; other site 358220008507 Walker B; other site 358220008508 D-loop; other site 358220008509 H-loop/switch region; other site 358220008510 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220008511 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220008512 Walker A/P-loop; other site 358220008513 ATP binding site [chemical binding]; other site 358220008514 Q-loop/lid; other site 358220008515 ABC transporter signature motif; other site 358220008516 Walker B; other site 358220008517 D-loop; other site 358220008518 H-loop/switch region; other site 358220008519 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220008520 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220008521 TM-ABC transporter signature motif; other site 358220008522 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220008523 TM-ABC transporter signature motif; other site 358220008524 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220008525 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 358220008526 putative ligand binding site [chemical binding]; other site 358220008527 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 358220008528 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 358220008529 dimer interface [polypeptide binding]; other site 358220008530 acyl-activating enzyme (AAE) consensus motif; other site 358220008531 putative active site [active] 358220008532 AMP binding site [chemical binding]; other site 358220008533 putative CoA binding site [chemical binding]; other site 358220008534 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220008535 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220008536 ligand binding site [chemical binding]; other site 358220008537 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 358220008538 non-specific DNA interactions [nucleotide binding]; other site 358220008539 DNA binding site [nucleotide binding] 358220008540 sequence specific DNA binding site [nucleotide binding]; other site 358220008541 putative cAMP binding site [chemical binding]; other site 358220008542 Carboxylesterase family; Region: COesterase; pfam00135 358220008543 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 358220008544 substrate binding pocket [chemical binding]; other site 358220008545 catalytic triad [active] 358220008546 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 358220008547 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 358220008548 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220008549 hypothetical protein; Validated; Region: PRK00029 358220008550 Uncharacterized conserved protein [Function unknown]; Region: COG0397 358220008551 methionine sulfoxide reductase B; Provisional; Region: PRK00222 358220008552 SelR domain; Region: SelR; pfam01641 358220008553 intracellular septation protein A; Reviewed; Region: PRK00259 358220008554 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 358220008555 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 358220008556 Protein of unknown function (DUF1624); Region: DUF1624; pfam07786 358220008557 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 358220008558 rRNA binding site [nucleotide binding]; other site 358220008559 predicted 30S ribosome binding site; other site 358220008560 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 358220008561 HPP family; Region: HPP; pfam04982 358220008562 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 358220008563 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220008564 Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; Region: PBP1_alkylbenzenes_like; cd06360 358220008565 putative ligand binding site [chemical binding]; other site 358220008566 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220008567 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220008568 TM-ABC transporter signature motif; other site 358220008569 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220008570 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220008571 TM-ABC transporter signature motif; other site 358220008572 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220008573 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220008574 Walker A/P-loop; other site 358220008575 ATP binding site [chemical binding]; other site 358220008576 Q-loop/lid; other site 358220008577 ABC transporter signature motif; other site 358220008578 Walker B; other site 358220008579 D-loop; other site 358220008580 H-loop/switch region; other site 358220008581 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220008582 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220008583 Walker A/P-loop; other site 358220008584 ATP binding site [chemical binding]; other site 358220008585 Q-loop/lid; other site 358220008586 ABC transporter signature motif; other site 358220008587 Walker B; other site 358220008588 D-loop; other site 358220008589 H-loop/switch region; other site 358220008590 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 358220008591 N-formylglutamate amidohydrolase; Region: FGase; cl01522 358220008592 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 358220008593 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 358220008594 active site 358220008595 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 358220008596 imidazolonepropionase; Region: hutI; TIGR01224 358220008597 active site 358220008598 HutD; Region: HutD; pfam05962 358220008599 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 358220008600 urocanate hydratase; Provisional; Region: PRK05414 358220008601 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 358220008602 active sites [active] 358220008603 tetramer interface [polypeptide binding]; other site 358220008604 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 358220008605 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220008606 DNA-binding site [nucleotide binding]; DNA binding site 358220008607 UTRA domain; Region: UTRA; pfam07702 358220008608 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 358220008609 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 358220008610 Walker A/P-loop; other site 358220008611 ATP binding site [chemical binding]; other site 358220008612 Q-loop/lid; other site 358220008613 ABC transporter signature motif; other site 358220008614 Walker B; other site 358220008615 D-loop; other site 358220008616 H-loop/switch region; other site 358220008617 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 358220008618 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220008619 dimer interface [polypeptide binding]; other site 358220008620 conserved gate region; other site 358220008621 putative PBP binding loops; other site 358220008622 ABC-ATPase subunit interface; other site 358220008623 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 358220008624 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220008625 substrate binding pocket [chemical binding]; other site 358220008626 membrane-bound complex binding site; other site 358220008627 hinge residues; other site 358220008628 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220008629 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220008630 dimerization interface [polypeptide binding]; other site 358220008631 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220008632 dimer interface [polypeptide binding]; other site 358220008633 phosphorylation site [posttranslational modification] 358220008634 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220008635 ATP binding site [chemical binding]; other site 358220008636 G-X-G motif; other site 358220008637 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220008638 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220008639 active site 358220008640 phosphorylation site [posttranslational modification] 358220008641 intermolecular recognition site; other site 358220008642 dimerization interface [polypeptide binding]; other site 358220008643 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220008644 DNA binding site [nucleotide binding] 358220008645 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 358220008646 dimer interface [polypeptide binding]; other site 358220008647 phosphoglycolate phosphatase; Provisional; Region: PRK13222 358220008648 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 358220008649 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 358220008650 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220008651 S-adenosylmethionine binding site [chemical binding]; other site 358220008652 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 358220008653 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 358220008654 ligand binding site [chemical binding]; other site 358220008655 DNA gyrase subunit A; Validated; Region: PRK05560 358220008656 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 358220008657 CAP-like domain; other site 358220008658 active site 358220008659 primary dimer interface [polypeptide binding]; other site 358220008660 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 358220008661 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 358220008662 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 358220008663 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 358220008664 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 358220008665 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 358220008666 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 358220008667 homodimer interface [polypeptide binding]; other site 358220008668 substrate-cofactor binding pocket; other site 358220008669 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220008670 catalytic residue [active] 358220008671 Chorismate mutase type II; Region: CM_2; pfam01817 358220008672 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 358220008673 Prephenate dehydratase; Region: PDT; pfam00800 358220008674 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 358220008675 putative L-Phe binding site [chemical binding]; other site 358220008676 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 358220008677 prephenate dehydrogenase; Validated; Region: PRK08507 358220008678 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 358220008679 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 358220008680 hinge; other site 358220008681 active site 358220008682 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 358220008683 CMP-binding site; other site 358220008684 The sites determining sugar specificity; other site 358220008685 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 358220008686 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 358220008687 RNA binding site [nucleotide binding]; other site 358220008688 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 358220008689 RNA binding site [nucleotide binding]; other site 358220008690 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 358220008691 RNA binding site [nucleotide binding]; other site 358220008692 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 358220008693 RNA binding site [nucleotide binding]; other site 358220008694 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 358220008695 RNA binding site [nucleotide binding]; other site 358220008696 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 358220008697 RNA binding site [nucleotide binding]; other site 358220008698 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 358220008699 IHF dimer interface [polypeptide binding]; other site 358220008700 IHF - DNA interface [nucleotide binding]; other site 358220008701 tetratricopeptide repeat protein; Provisional; Region: PRK11788 358220008702 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 358220008703 binding surface 358220008704 TPR motif; other site 358220008705 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 358220008706 DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]; Region: DnaE; COG0587 358220008707 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 358220008708 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 358220008709 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 358220008710 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 358220008711 monovalent cation:proton antiporter; Region: 2a6301s02; TIGR00943 358220008712 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK09094 358220008713 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 358220008714 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 358220008715 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 358220008716 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 358220008717 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 358220008718 5-oxoprolinase; Region: PLN02666 358220008719 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 358220008720 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 358220008721 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 358220008722 MarR family; Region: MarR_2; cl17246 358220008723 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220008724 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 358220008725 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 358220008726 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 358220008727 DctM-like transporters; Region: DctM; pfam06808 358220008728 chromosome condensation membrane protein; Provisional; Region: PRK14196 358220008729 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 358220008730 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220008731 putative substrate translocation pore; other site 358220008732 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220008733 RmuC family; Region: RmuC; pfam02646 358220008734 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 358220008735 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 358220008736 dimerization interface [polypeptide binding]; other site 358220008737 ligand binding site [chemical binding]; other site 358220008738 NADP binding site [chemical binding]; other site 358220008739 catalytic site [active] 358220008740 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 358220008741 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 358220008742 transmembrane helices; other site 358220008743 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 358220008744 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting; Region: PncB_like; cd01401 358220008745 active site 358220008746 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 358220008747 active site 358220008748 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 358220008749 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 358220008750 putative active site [active] 358220008751 Zn binding site [ion binding]; other site 358220008752 Phasin protein; Region: Phasin_2; pfam09361 358220008753 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 358220008754 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 358220008755 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 358220008756 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 358220008757 NAD binding site [chemical binding]; other site 358220008758 homodimer interface [polypeptide binding]; other site 358220008759 homotetramer interface [polypeptide binding]; other site 358220008760 active site 358220008761 PAS fold; Region: PAS_4; pfam08448 358220008762 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220008763 putative active site [active] 358220008764 heme pocket [chemical binding]; other site 358220008765 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220008766 PAS domain; Region: PAS_9; pfam13426 358220008767 putative active site [active] 358220008768 heme pocket [chemical binding]; other site 358220008769 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220008770 metal binding site [ion binding]; metal-binding site 358220008771 active site 358220008772 I-site; other site 358220008773 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220008774 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 358220008775 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 358220008776 active site 358220008777 HIGH motif; other site 358220008778 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 358220008779 active site 358220008780 KMSKS motif; other site 358220008781 amidophosphoribosyltransferase; Provisional; Region: PRK09246 358220008782 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 358220008783 active site 358220008784 tetramer interface [polypeptide binding]; other site 358220008785 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220008786 active site 358220008787 Colicin V production protein; Region: Colicin_V; pfam02674 358220008788 Sporulation related domain; Region: SPOR; pfam05036 358220008789 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 358220008790 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 358220008791 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 358220008792 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 358220008793 ArsC family; Region: ArsC; pfam03960 358220008794 putative catalytic residues [active] 358220008795 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 358220008796 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 358220008797 argininosuccinate synthase; Validated; Region: PRK05370 358220008798 argininosuccinate synthase; Provisional; Region: PRK13820 358220008799 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 358220008800 FAD binding domain; Region: FAD_binding_4; pfam01565 358220008801 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 358220008802 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 358220008803 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 358220008804 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 358220008805 catalytic motif [active] 358220008806 Catalytic residue [active] 358220008807 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 358220008808 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 358220008809 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 358220008810 putative deacylase active site [active] 358220008811 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220008812 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220008813 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220008814 dimerization interface [polypeptide binding]; other site 358220008815 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220008816 hypothetical protein; Provisional; Region: PRK07079 358220008817 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_2; cd05679 358220008818 metal binding site [ion binding]; metal-binding site 358220008819 putative dimer interface [polypeptide binding]; other site 358220008820 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 358220008821 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 358220008822 active site 358220008823 catalytic tetrad [active] 358220008824 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 358220008825 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 358220008826 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 358220008827 catalytic site [active] 358220008828 potential frameshift: common BLAST hit: gi|326316598|ref|YP_004234270.1| peptide chain release factor 2 358220008829 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 358220008830 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220008831 motif II; other site 358220008832 aminopeptidase N; Provisional; Region: pepN; PRK14015 358220008833 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 358220008834 active site 358220008835 Zn binding site [ion binding]; other site 358220008836 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 358220008837 AMP binding site [chemical binding]; other site 358220008838 metal binding site [ion binding]; metal-binding site 358220008839 active site 358220008840 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 358220008841 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 358220008842 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220008843 ATP binding site [chemical binding]; other site 358220008844 putative Mg++ binding site [ion binding]; other site 358220008845 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220008846 nucleotide binding region [chemical binding]; other site 358220008847 ATP-binding site [chemical binding]; other site 358220008848 Predicted transcriptional regulator [Transcription]; Region: COG2378 358220008849 WYL domain; Region: WYL; pfam13280 358220008850 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 358220008851 active site 358220008852 metal binding site [ion binding]; metal-binding site 358220008853 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 358220008854 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 358220008855 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 358220008856 Family description; Region: UvrD_C_2; pfam13538 358220008857 DEAD-like helicases superfamily; Region: DEXDc; smart00487 358220008858 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220008859 ATP binding site [chemical binding]; other site 358220008860 putative Mg++ binding site [ion binding]; other site 358220008861 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220008862 ATP-binding site [chemical binding]; other site 358220008863 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 358220008864 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 358220008865 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 358220008866 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220008867 ATP binding site [chemical binding]; other site 358220008868 putative Mg++ binding site [ion binding]; other site 358220008869 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220008870 nucleotide binding region [chemical binding]; other site 358220008871 ATP-binding site [chemical binding]; other site 358220008872 phage/plasmid primase, P4 family, C-terminal domain; Region: primase_Cterm; TIGR01613 358220008873 Poxvirus D5 protein-like; Region: Pox_D5; pfam03288 358220008874 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 358220008875 Protein of unknown function (DUF497); Region: DUF497; pfam04365 358220008876 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 358220008877 nudix motif; other site 358220008878 conserved hypothetical protein; Region: Lon_rel_chp; TIGR02653 358220008879 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220008880 active site 358220008881 Int/Topo IB signature motif; other site 358220008882 DNA binding site [nucleotide binding] 358220008883 integrase; Provisional; Region: int; PHA02601 358220008884 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220008885 active site 358220008886 DNA binding site [nucleotide binding] 358220008887 Int/Topo IB signature motif; other site 358220008888 Transposase domain (DUF772); Region: DUF772; pfam05598 358220008889 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 358220008890 DDE superfamily endonuclease; Region: DDE_4; cl17710 358220008891 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 358220008892 DNA binding site [nucleotide binding] 358220008893 dimer interface [polypeptide binding]; other site 358220008894 active site 358220008895 Int/Topo IB signature motif; other site 358220008896 Protein of unknown function DUF45; Region: DUF45; pfam01863 358220008897 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 358220008898 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 358220008899 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220008900 ATP binding site [chemical binding]; other site 358220008901 putative Mg++ binding site [ion binding]; other site 358220008902 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 358220008903 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 358220008904 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 358220008905 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 358220008906 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 358220008907 HsdM N-terminal domain; Region: HsdM_N; pfam12161 358220008908 Methyltransferase domain; Region: Methyltransf_26; pfam13659 358220008909 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 358220008910 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 358220008911 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 358220008912 Phage replication protein CRI; Region: Phage_CRI; pfam05144 358220008913 AAA domain; Region: AAA_25; pfam13481 358220008914 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220008915 Walker A motif; other site 358220008916 ATP binding site [chemical binding]; other site 358220008917 Walker B motif; other site 358220008918 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220008919 salt bridge; other site 358220008920 non-specific DNA binding site [nucleotide binding]; other site 358220008921 sequence-specific DNA binding site [nucleotide binding]; other site 358220008922 VRR-NUC domain; Region: VRR_NUC; pfam08774 358220008923 Primase C terminal 2 (PriCT-2); Region: PriCT_2; pfam08707 358220008924 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 358220008925 AAA domain; Region: AAA_25; pfam13481 358220008926 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220008927 Walker A motif; other site 358220008928 ATP binding site [chemical binding]; other site 358220008929 Walker B motif; other site 358220008930 Helix-turn-helix domain; Region: HTH_39; pfam14090 358220008931 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220008932 active site 358220008933 Int/Topo IB signature motif; other site 358220008934 DNA binding site [nucleotide binding] 358220008935 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 358220008936 ssDNA binding site [nucleotide binding]; other site 358220008937 tetramer (dimer of dimers) interface [polypeptide binding]; other site 358220008938 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 358220008939 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 358220008940 DNA binding residues [nucleotide binding] 358220008941 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 358220008942 IHF - DNA interface [nucleotide binding]; other site 358220008943 IHF dimer interface [polypeptide binding]; other site 358220008944 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 358220008945 tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate...; Region: tRNA_bind_bactPheRS; cd02796 358220008946 putative tRNA-binding site [nucleotide binding]; other site 358220008947 B3/4 domain; Region: B3_4; pfam03483 358220008948 tRNA synthetase B5 domain; Region: B5; smart00874 358220008949 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an...; Region: PheRS_beta_core; cd00769 358220008950 dimer interface [polypeptide binding]; other site 358220008951 motif 1; other site 358220008952 motif 3; other site 358220008953 motif 2; other site 358220008954 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 358220008955 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 358220008956 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 358220008957 Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible...; Region: PheRS_alpha_core; cd00496 358220008958 dimer interface [polypeptide binding]; other site 358220008959 motif 1; other site 358220008960 active site 358220008961 motif 2; other site 358220008962 motif 3; other site 358220008963 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 358220008964 23S rRNA binding site [nucleotide binding]; other site 358220008965 L21 binding site [polypeptide binding]; other site 358220008966 L13 binding site [polypeptide binding]; other site 358220008967 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 358220008968 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 358220008969 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 358220008970 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 358220008971 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 358220008972 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 358220008973 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 358220008974 Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ThrRS_core; cd00771 358220008975 active site 358220008976 dimer interface [polypeptide binding]; other site 358220008977 motif 1; other site 358220008978 motif 2; other site 358220008979 motif 3; other site 358220008980 ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: ThrRS_anticodon; cd00860 358220008981 anticodon binding site; other site 358220008982 isocitrate lyase; Provisional; Region: PRK15063 358220008983 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 358220008984 tetramer interface [polypeptide binding]; other site 358220008985 active site 358220008986 Mg2+/Mn2+ binding site [ion binding]; other site 358220008987 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 358220008988 putative active site pocket [active] 358220008989 dimerization interface [polypeptide binding]; other site 358220008990 putative catalytic residue [active] 358220008991 EamA-like transporter family; Region: EamA; pfam00892 358220008992 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 358220008993 EamA-like transporter family; Region: EamA; pfam00892 358220008994 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 358220008995 SWI complex, BAF60b domains; Region: SWIB; smart00151 358220008996 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 358220008997 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 358220008998 N-terminal plug; other site 358220008999 ligand-binding site [chemical binding]; other site 358220009000 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 358220009001 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 358220009002 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 358220009003 active site 358220009004 substrate binding site [chemical binding]; other site 358220009005 FMN binding site [chemical binding]; other site 358220009006 putative catalytic residues [active] 358220009007 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 358220009008 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 358220009009 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 358220009010 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 358220009011 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 358220009012 TolR protein; Region: tolR; TIGR02801 358220009013 Hemin uptake protein hemP; Region: hemP; pfam10636 358220009014 Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only]; Region: GlcG; COG3193 358220009015 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 358220009016 YccA-like proteins; Region: YccA_like; cd10433 358220009017 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 358220009018 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220009019 S-adenosylmethionine binding site [chemical binding]; other site 358220009020 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 358220009021 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220009022 putative DNA binding site [nucleotide binding]; other site 358220009023 putative Zn2+ binding site [ion binding]; other site 358220009024 AsnC family; Region: AsnC_trans_reg; pfam01037 358220009025 trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: putA; PRK11809 358220009026 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 358220009027 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 358220009028 Glutamate binding site [chemical binding]; other site 358220009029 NAD binding site [chemical binding]; other site 358220009030 catalytic residues [active] 358220009031 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 358220009032 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cl00365 358220009033 Protein of unknown function (DUF3732); Region: DUF3732; pfam12532 358220009034 Uncharacterized conserved small protein [Function unknown]; Region: COG5639 358220009035 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 358220009036 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 358220009037 VirB7 interaction site; other site 358220009038 conjugal transfer protein TrbF; Provisional; Region: PRK13872 358220009039 conjugal transfer protein TrbL; Provisional; Region: PRK13875 358220009040 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 358220009041 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 358220009042 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 358220009043 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 358220009044 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 358220009045 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220009046 Walker A motif; other site 358220009047 ATP binding site [chemical binding]; other site 358220009048 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 358220009049 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 358220009050 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 358220009051 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 358220009052 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 358220009053 ATP binding site [chemical binding]; other site 358220009054 Walker A motif; other site 358220009055 hexamer interface [polypeptide binding]; other site 358220009056 Walker B motif; other site 358220009057 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 358220009058 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 358220009059 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220009060 Walker A motif; other site 358220009061 ATP binding site [chemical binding]; other site 358220009062 Walker B motif; other site 358220009063 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220009064 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220009065 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 358220009066 dimerization interface [polypeptide binding]; other site 358220009067 substrate binding pocket [chemical binding]; other site 358220009068 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 358220009069 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 358220009070 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 358220009071 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 358220009072 Ligand binding site [chemical binding]; other site 358220009073 Electron transfer flavoprotein domain; Region: ETF; pfam01012 358220009074 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 358220009075 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220009076 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220009077 active site 358220009078 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 358220009079 benzoate transport; Region: 2A0115; TIGR00895 358220009080 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220009081 putative substrate translocation pore; other site 358220009082 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220009083 DDE superfamily endonuclease; Region: DDE_3; pfam13358 358220009084 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 358220009085 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 358220009086 Helix-turn-helix domain; Region: HTH_18; pfam12833 358220009087 SurA N-terminal domain; Region: SurA_N; pfam09312 358220009088 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220009089 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220009090 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220009091 active site 358220009092 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 358220009093 CoA-transferase family III; Region: CoA_transf_3; pfam02515 358220009094 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 358220009095 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 358220009096 dimer interface [polypeptide binding]; other site 358220009097 acyl-activating enzyme (AAE) consensus motif; other site 358220009098 putative active site [active] 358220009099 AMP binding site [chemical binding]; other site 358220009100 putative CoA binding site [chemical binding]; other site 358220009101 acetyl-CoA acetyltransferase; Provisional; Region: PRK07801 358220009102 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220009103 dimer interface [polypeptide binding]; other site 358220009104 active site 358220009105 enoyl-CoA hydratase; Provisional; Region: PRK08138 358220009106 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220009107 substrate binding site [chemical binding]; other site 358220009108 oxyanion hole (OAH) forming residues; other site 358220009109 trimer interface [polypeptide binding]; other site 358220009110 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220009111 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 358220009112 NAD(P) binding site [chemical binding]; other site 358220009113 active site 358220009114 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 358220009115 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220009116 substrate binding site [chemical binding]; other site 358220009117 oxyanion hole (OAH) forming residues; other site 358220009118 trimer interface [polypeptide binding]; other site 358220009119 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 358220009120 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 358220009121 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 358220009122 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 358220009123 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 358220009124 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 358220009125 ParA-like protein; Provisional; Region: PHA02518 358220009126 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 358220009127 P-loop; other site 358220009128 Magnesium ion binding site [ion binding]; other site 358220009129 Replication initiator protein A; Region: RPA; pfam10134 358220009130 Helix-turn-helix domain; Region: HTH_17; cl17695 358220009131 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 358220009132 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 358220009133 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220009134 non-specific DNA binding site [nucleotide binding]; other site 358220009135 salt bridge; other site 358220009136 sequence-specific DNA binding site [nucleotide binding]; other site 358220009137 Uncharacterized conserved protein [Function unknown]; Region: COG5489 358220009138 isocitrate lyase; Provisional; Region: PRK15063 358220009139 ParB-like nuclease domain; Region: ParBc; pfam02195 358220009140 Domain of unknown function (DUF932); Region: DUF932; pfam06067 358220009141 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 358220009142 Restriction endonuclease; Region: Mrr_cat; pfam04471 358220009143 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 358220009144 Abortive infection C-terminus; Region: Abi_C; pfam14355 358220009145 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 358220009146 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 358220009147 active site 358220009148 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 358220009149 nucleotide binding site/active site [active] 358220009150 HIT family signature motif; other site 358220009151 catalytic residue [active] 358220009152 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 358220009153 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 358220009154 active site 358220009155 catalytic site [active] 358220009156 substrate binding site [chemical binding]; other site 358220009157 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 358220009158 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220009159 ATP binding site [chemical binding]; other site 358220009160 putative Mg++ binding site [ion binding]; other site 358220009161 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220009162 nucleotide binding region [chemical binding]; other site 358220009163 ATP-binding site [chemical binding]; other site 358220009164 DEAD-like helicases superfamily; Region: DEXDc; smart00487 358220009165 Part of AAA domain; Region: AAA_19; pfam13245 358220009166 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 358220009167 Family description; Region: UvrD_C_2; pfam13538 358220009168 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 358220009169 PLD-like domain; Region: PLDc_2; pfam13091 358220009170 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 358220009171 putative active site [active] 358220009172 catalytic site [active] 358220009173 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 358220009174 putative active site [active] 358220009175 catalytic site [active] 358220009176 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 358220009177 Protein of unknwon function (DUF2893); Region: DUF2893; pfam11459 358220009178 integrase; Provisional; Region: PRK09692 358220009179 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 358220009180 active site 358220009181 Int/Topo IB signature motif; other site 358220009182 GMP synthase; Reviewed; Region: guaA; PRK00074 358220009183 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 358220009184 AMP/PPi binding site [chemical binding]; other site 358220009185 candidate oxyanion hole; other site 358220009186 catalytic triad [active] 358220009187 potential glutamine specificity residues [chemical binding]; other site 358220009188 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 358220009189 ATP Binding subdomain [chemical binding]; other site 358220009190 Ligand Binding sites [chemical binding]; other site 358220009191 Dimerization subdomain; other site 358220009192 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 358220009193 putative active site [active] 358220009194 homotetrameric interface [polypeptide binding]; other site 358220009195 metal binding site [ion binding]; metal-binding site 358220009196 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 358220009197 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 358220009198 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 358220009199 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 358220009200 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 358220009201 active site 358220009202 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 358220009203 RnfH family Ubiquitin; Region: Ub-RnfH; cl17382 358220009204 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 358220009205 putative coenzyme Q binding site [chemical binding]; other site 358220009206 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 358220009207 SmpB-tmRNA interface; other site 358220009208 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 358220009209 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 358220009210 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220009211 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220009212 DNA binding residues [nucleotide binding] 358220009213 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 358220009214 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 358220009215 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220009216 substrate binding site [chemical binding]; other site 358220009217 oxyanion hole (OAH) forming residues; other site 358220009218 trimer interface [polypeptide binding]; other site 358220009219 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 358220009220 EamA-like transporter family; Region: EamA; pfam00892 358220009221 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 358220009222 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 358220009223 G1 box; other site 358220009224 putative GEF interaction site [polypeptide binding]; other site 358220009225 GTP/Mg2+ binding site [chemical binding]; other site 358220009226 Switch I region; other site 358220009227 G2 box; other site 358220009228 G3 box; other site 358220009229 Switch II region; other site 358220009230 G4 box; other site 358220009231 G5 box; other site 358220009232 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 358220009233 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 358220009234 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01851 358220009235 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 358220009236 RNA binding site [nucleotide binding]; other site 358220009237 active site 358220009238 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 358220009239 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 358220009240 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 358220009241 translation initiation factor IF-2; Region: IF-2; TIGR00487 358220009242 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 358220009243 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 358220009244 G1 box; other site 358220009245 putative GEF interaction site [polypeptide binding]; other site 358220009246 GTP/Mg2+ binding site [chemical binding]; other site 358220009247 Switch I region; other site 358220009248 G2 box; other site 358220009249 G3 box; other site 358220009250 Switch II region; other site 358220009251 G4 box; other site 358220009252 G5 box; other site 358220009253 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 358220009254 Translation-initiation factor 2; Region: IF-2; pfam11987 358220009255 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 358220009256 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 358220009257 NusA N-terminal domain; Region: NusA_N; pfam08529 358220009258 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 358220009259 RNA binding site [nucleotide binding]; other site 358220009260 homodimer interface [polypeptide binding]; other site 358220009261 NusA-like KH domain; Region: KH_5; pfam13184 358220009262 NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of...; Region: NusA_KH; cd02134 358220009263 G-X-X-G motif; other site 358220009264 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 358220009265 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 358220009266 ribosome maturation protein RimP; Reviewed; Region: PRK00092 358220009267 Sm and related proteins; Region: Sm_like; cl00259 358220009268 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 358220009269 putative RNA binding site [nucleotide binding]; other site 358220009270 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 358220009271 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220009272 ATP binding site [chemical binding]; other site 358220009273 putative Mg++ binding site [ion binding]; other site 358220009274 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220009275 nucleotide binding region [chemical binding]; other site 358220009276 ATP-binding site [chemical binding]; other site 358220009277 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 358220009278 catalytic residues [active] 358220009279 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 358220009280 Cytochrome c; Region: Cytochrom_C; pfam00034 358220009281 Cytochrome c; Region: Cytochrom_C; cl11414 358220009282 Cytochrome c; Region: Cytochrom_C; cl11414 358220009283 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 358220009284 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220009285 DNA-binding site [nucleotide binding]; DNA binding site 358220009286 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220009287 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220009288 homodimer interface [polypeptide binding]; other site 358220009289 catalytic residue [active] 358220009290 potential frameshift: common BLAST hit: gi|264678043|ref|YP_003277950.1| diguanylate cyclase 358220009291 putative oxidoreductase/HEAT repeat-containing protein; Provisional; Region: PRK13800 358220009292 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 358220009293 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 358220009294 catalytic residues [active] 358220009295 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 358220009296 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220009297 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220009298 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220009299 putative effector binding pocket; other site 358220009300 dimerization interface [polypeptide binding]; other site 358220009301 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220009302 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 358220009303 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 358220009304 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220009305 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 358220009306 putative dimerization interface [polypeptide binding]; other site 358220009307 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 358220009308 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 358220009309 hypothetical protein; Provisional; Region: PRK14812 358220009310 substrate binding site [chemical binding]; other site 358220009311 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 358220009312 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 358220009313 substrate binding site [chemical binding]; other site 358220009314 ligand binding site [chemical binding]; other site 358220009315 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220009316 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220009317 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220009318 transcriptional activator TtdR; Provisional; Region: PRK09801 358220009319 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 358220009320 putative effector binding pocket; other site 358220009321 putative dimerization interface [polypeptide binding]; other site 358220009322 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 358220009323 outer membrane lipoprotein Blc; Provisional; Region: PRK10477 358220009324 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 358220009325 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 358220009326 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 358220009327 Walker A/P-loop; other site 358220009328 ATP binding site [chemical binding]; other site 358220009329 Q-loop/lid; other site 358220009330 ABC transporter signature motif; other site 358220009331 Walker B; other site 358220009332 D-loop; other site 358220009333 H-loop/switch region; other site 358220009334 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 358220009335 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 358220009336 Walker A/P-loop; other site 358220009337 ATP binding site [chemical binding]; other site 358220009338 Q-loop/lid; other site 358220009339 ABC transporter signature motif; other site 358220009340 Walker B; other site 358220009341 D-loop; other site 358220009342 H-loop/switch region; other site 358220009343 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 358220009344 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 358220009345 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 358220009346 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220009347 dimer interface [polypeptide binding]; other site 358220009348 conserved gate region; other site 358220009349 putative PBP binding loops; other site 358220009350 ABC-ATPase subunit interface; other site 358220009351 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 358220009352 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220009353 dimer interface [polypeptide binding]; other site 358220009354 conserved gate region; other site 358220009355 ABC-ATPase subunit interface; other site 358220009356 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 358220009357 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 358220009358 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 358220009359 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 358220009360 NAD binding site [chemical binding]; other site 358220009361 homotetramer interface [polypeptide binding]; other site 358220009362 homodimer interface [polypeptide binding]; other site 358220009363 substrate binding site [chemical binding]; other site 358220009364 active site 358220009365 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 358220009366 DNA binding site [nucleotide binding] 358220009367 DNA polymerase LigD, ligase domain; Region: NHEJ_ligase_lig; TIGR02779 358220009368 active site 358220009369 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 358220009370 DNA binding site [nucleotide binding] 358220009371 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 358220009372 Fasciclin domain; Region: Fasciclin; pfam02469 358220009373 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 358220009374 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 358220009375 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 358220009376 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220009377 catalytic residue [active] 358220009378 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 358220009379 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 358220009380 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 358220009381 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220009382 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220009383 S-adenosylmethionine binding site [chemical binding]; other site 358220009384 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 358220009385 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 358220009386 catalytic residues [active] 358220009387 catalytic nucleophile [active] 358220009388 Presynaptic Site I dimer interface [polypeptide binding]; other site 358220009389 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 358220009390 Synaptic Flat tetramer interface [polypeptide binding]; other site 358220009391 Synaptic Site I dimer interface [polypeptide binding]; other site 358220009392 DNA binding site [nucleotide binding] 358220009393 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 358220009394 mce related protein; Region: MCE; pfam02470 358220009395 Permease; Region: Permease; pfam02405 358220009396 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 358220009397 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 358220009398 DNA binding residues [nucleotide binding] 358220009399 dimer interface [polypeptide binding]; other site 358220009400 putative metal binding site [ion binding]; other site 358220009401 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 358220009402 Protein of unknown function (DUF3703); Region: DUF3703; pfam12487 358220009403 Uncharacterized conserved protein [Function unknown]; Region: COG1284 358220009404 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220009405 dimerization interface [polypeptide binding]; other site 358220009406 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220009407 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220009408 putative active site [active] 358220009409 heme pocket [chemical binding]; other site 358220009410 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220009411 putative active site [active] 358220009412 heme pocket [chemical binding]; other site 358220009413 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220009414 PAS domain; Region: PAS_9; pfam13426 358220009415 putative active site [active] 358220009416 heme pocket [chemical binding]; other site 358220009417 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220009418 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220009419 metal binding site [ion binding]; metal-binding site 358220009420 active site 358220009421 I-site; other site 358220009422 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220009423 urease accessory protein UreE; Provisional; Region: ureE; PRK13263 358220009424 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 358220009425 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 358220009426 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 358220009427 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 358220009428 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 358220009429 Predicted metal-binding protein [General function prediction only]; Region: COG3019 358220009430 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 358220009431 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 358220009432 putative active site pocket [active] 358220009433 cleavage site 358220009434 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220009435 Coenzyme A binding pocket [chemical binding]; other site 358220009436 Ricin-type beta-trefoil lectin domain; Region: Ricin_B_lectin; pfam00652 358220009437 Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific...; Region: RICIN; cd00161 358220009438 putative sugar binding sites [chemical binding]; other site 358220009439 Q-X-W motif; other site 358220009440 EF-hand domain pair; Region: EF_hand_5; pfam13499 358220009441 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 358220009442 Ca2+ binding site [ion binding]; other site 358220009443 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 358220009444 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 358220009445 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 358220009446 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 358220009447 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 358220009448 ABC transporter; Region: ABC_tran_2; pfam12848 358220009449 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 358220009450 helicase 45; Provisional; Region: PTZ00424 358220009451 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 358220009452 ATP binding site [chemical binding]; other site 358220009453 Mg++ binding site [ion binding]; other site 358220009454 motif III; other site 358220009455 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220009456 nucleotide binding region [chemical binding]; other site 358220009457 ATP-binding site [chemical binding]; other site 358220009458 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 358220009459 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220009460 NAD(P) binding site [chemical binding]; other site 358220009461 active site 358220009462 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 358220009463 putative catalytic site [active] 358220009464 putative metal binding site [ion binding]; other site 358220009465 putative phosphate binding site [ion binding]; other site 358220009466 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 358220009467 active site 358220009468 Zn binding site [ion binding]; other site 358220009469 putative cation:proton antiport protein; Provisional; Region: PRK10669 358220009470 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 358220009471 TrkA-N domain; Region: TrkA_N; pfam02254 358220009472 periplasmic folding chaperone; Provisional; Region: PRK10788 358220009473 SurA N-terminal domain; Region: SurA_N_3; cl07813 358220009474 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 358220009475 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 358220009476 IHF dimer interface [polypeptide binding]; other site 358220009477 IHF - DNA interface [nucleotide binding]; other site 358220009478 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 358220009479 tartrate dehydrogenase; Region: TTC; TIGR02089 358220009480 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 358220009481 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 358220009482 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 358220009483 GIY-YIG motif/motif A; other site 358220009484 active site 358220009485 catalytic site [active] 358220009486 putative DNA binding site [nucleotide binding]; other site 358220009487 metal binding site [ion binding]; metal-binding site 358220009488 UvrB/uvrC motif; Region: UVR; pfam02151 358220009489 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 358220009490 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 358220009491 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220009492 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 358220009493 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 358220009494 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 358220009495 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220009496 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 358220009497 active site 358220009498 catalytic residues [active] 358220009499 metal binding site [ion binding]; metal-binding site 358220009500 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 358220009501 CoA-transferase family III; Region: CoA_transf_3; pfam02515 358220009502 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220009503 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220009504 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 358220009505 putative dimerization interface [polypeptide binding]; other site 358220009506 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 358220009507 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 358220009508 elongation factor P; Validated; Region: PRK00529 358220009509 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 358220009510 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 358220009511 RNA binding site [nucleotide binding]; other site 358220009512 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 358220009513 RNA binding site [nucleotide binding]; other site 358220009514 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 358220009515 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 358220009516 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220009517 FeS/SAM binding site; other site 358220009518 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 358220009519 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 358220009520 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 358220009521 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 358220009522 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 358220009523 HD domain; Region: HD_4; pfam13328 358220009524 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 358220009525 synthetase active site [active] 358220009526 NTP binding site [chemical binding]; other site 358220009527 metal binding site [ion binding]; metal-binding site 358220009528 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 358220009529 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 358220009530 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220009531 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 358220009532 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220009533 NAD(P) binding site [chemical binding]; other site 358220009534 active site 358220009535 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 358220009536 osmolarity response regulator; Provisional; Region: ompR; PRK09468 358220009537 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220009538 active site 358220009539 phosphorylation site [posttranslational modification] 358220009540 intermolecular recognition site; other site 358220009541 dimerization interface [polypeptide binding]; other site 358220009542 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220009543 DNA binding site [nucleotide binding] 358220009544 HAMP domain; Region: HAMP; pfam00672 358220009545 dimerization interface [polypeptide binding]; other site 358220009546 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220009547 dimer interface [polypeptide binding]; other site 358220009548 phosphorylation site [posttranslational modification] 358220009549 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220009550 ATP binding site [chemical binding]; other site 358220009551 Mg2+ binding site [ion binding]; other site 358220009552 G-X-G motif; other site 358220009553 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 358220009554 D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes; Region: D-glucarate_dehydratase; cd03323 358220009555 active site 358220009556 tetramer interface [polypeptide binding]; other site 358220009557 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220009558 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 358220009559 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH); Region: KDGDH; cd00951 358220009560 putative active site [active] 358220009561 catalytic residue [active] 358220009562 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 358220009563 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 358220009564 DNA binding site [nucleotide binding] 358220009565 domain linker motif; other site 358220009566 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 358220009567 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 358220009568 homotrimer interaction site [polypeptide binding]; other site 358220009569 zinc binding site [ion binding]; other site 358220009570 CDP-binding sites; other site 358220009571 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 358220009572 substrate binding site; other site 358220009573 dimer interface; other site 358220009574 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 358220009575 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 358220009576 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220009577 ATP binding site [chemical binding]; other site 358220009578 putative Mg++ binding site [ion binding]; other site 358220009579 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220009580 nucleotide binding region [chemical binding]; other site 358220009581 ATP-binding site [chemical binding]; other site 358220009582 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 358220009583 Predicted membrane protein [Function unknown]; Region: COG3235 358220009584 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 358220009585 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 358220009586 active site 358220009587 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 358220009588 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 358220009589 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220009590 motif II; other site 358220009591 Transcriptional regulator; Region: Rrf2; cl17282 358220009592 Rrf2 family protein; Region: rrf2_super; TIGR00738 358220009593 iron-sulfur cluster repair di-iron protein; Provisional; Region: PRK10992 358220009594 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 358220009595 Hemerythrin-like domain; Region: Hr-like; cd12108 358220009596 Fe binding site [ion binding]; other site 358220009597 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 358220009598 heme-binding site [chemical binding]; other site 358220009599 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 358220009600 translation initiation factor Sui1; Validated; Region: PRK06824 358220009601 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 358220009602 putative rRNA binding site [nucleotide binding]; other site 358220009603 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 358220009604 DEAD-like helicases superfamily; Region: DEXDc; smart00487 358220009605 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 358220009606 ATP binding site [chemical binding]; other site 358220009607 Mg++ binding site [ion binding]; other site 358220009608 motif III; other site 358220009609 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220009610 nucleotide binding region [chemical binding]; other site 358220009611 ATP-binding site [chemical binding]; other site 358220009612 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220009613 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 358220009614 putative active site [active] 358220009615 heme pocket [chemical binding]; other site 358220009616 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220009617 putative active site [active] 358220009618 heme pocket [chemical binding]; other site 358220009619 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220009620 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220009621 metal binding site [ion binding]; metal-binding site 358220009622 active site 358220009623 I-site; other site 358220009624 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220009625 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220009626 dimerization interface [polypeptide binding]; other site 358220009627 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220009628 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220009629 dimer interface [polypeptide binding]; other site 358220009630 putative CheW interface [polypeptide binding]; other site 358220009631 PBP superfamily domain; Region: PBP_like_2; cl17296 358220009632 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 358220009633 putative active site [active] 358220009634 putative metal binding residues [ion binding]; other site 358220009635 signature motif; other site 358220009636 putative triphosphate binding site [ion binding]; other site 358220009637 CHAD domain; Region: CHAD; pfam05235 358220009638 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 358220009639 catalytic site [active] 358220009640 putative active site [active] 358220009641 putative substrate binding site [chemical binding]; other site 358220009642 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 358220009643 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 358220009644 active site 358220009645 FMN binding site [chemical binding]; other site 358220009646 2,4-decadienoyl-CoA binding site; other site 358220009647 catalytic residue [active] 358220009648 4Fe-4S cluster binding site [ion binding]; other site 358220009649 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220009650 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220009651 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220009652 SlyX; Region: SlyX; pfam04102 358220009653 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 358220009654 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220009655 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220009656 homodimer interface [polypeptide binding]; other site 358220009657 catalytic residue [active] 358220009658 GyrI-like small molecule binding domain; Region: GyrI-like; pfam06445 358220009659 amidase; Provisional; Region: PRK07486 358220009660 Amidase; Region: Amidase; cl11426 358220009661 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220009662 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220009663 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220009664 dimerization interface [polypeptide binding]; other site 358220009665 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 358220009666 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 358220009667 minor groove reading motif; other site 358220009668 helix-hairpin-helix signature motif; other site 358220009669 substrate binding pocket [chemical binding]; other site 358220009670 active site 358220009671 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 358220009672 Prophage maintenance system killer protein [General function prediction only]; Region: Doc; COG3654 358220009673 putative addiction module antidote; Region: doc_partner; TIGR02609 358220009674 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 358220009675 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220009676 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220009677 DNA-binding site [nucleotide binding]; DNA binding site 358220009678 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 358220009679 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 358220009680 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220009681 dimer interface [polypeptide binding]; other site 358220009682 conserved gate region; other site 358220009683 putative PBP binding loops; other site 358220009684 ABC-ATPase subunit interface; other site 358220009685 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220009686 dimer interface [polypeptide binding]; other site 358220009687 conserved gate region; other site 358220009688 putative PBP binding loops; other site 358220009689 ABC-ATPase subunit interface; other site 358220009690 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 358220009691 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 358220009692 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220009693 Walker A/P-loop; other site 358220009694 ATP binding site [chemical binding]; other site 358220009695 Q-loop/lid; other site 358220009696 ABC transporter signature motif; other site 358220009697 Walker B; other site 358220009698 D-loop; other site 358220009699 H-loop/switch region; other site 358220009700 TOBE domain; Region: TOBE_2; pfam08402 358220009701 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220009702 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220009703 metal binding site [ion binding]; metal-binding site 358220009704 active site 358220009705 I-site; other site 358220009706 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 358220009707 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 358220009708 active site pocket [active] 358220009709 putative dimer interface [polypeptide binding]; other site 358220009710 putative cataytic base [active] 358220009711 Methyltransferase domain; Region: Methyltransf_11; pfam08241 358220009712 AAA domain; Region: AAA_26; pfam13500 358220009713 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 358220009714 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 358220009715 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 358220009716 catalytic triad [active] 358220009717 Protein of unknown function (DUF3037); Region: DUF3037; pfam11236 358220009718 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 358220009719 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 358220009720 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220009721 catalytic residue [active] 358220009722 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 358220009723 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 358220009724 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 358220009725 homodimer interface [polypeptide binding]; other site 358220009726 Walker A motif; other site 358220009727 ATP binding site [chemical binding]; other site 358220009728 hydroxycobalamin binding site [chemical binding]; other site 358220009729 Walker B motif; other site 358220009730 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 358220009731 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220009732 Walker A/P-loop; other site 358220009733 ATP binding site [chemical binding]; other site 358220009734 Q-loop/lid; other site 358220009735 ABC transporter signature motif; other site 358220009736 Walker B; other site 358220009737 D-loop; other site 358220009738 H-loop/switch region; other site 358220009739 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 358220009740 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 358220009741 dimer interface [polypeptide binding]; other site 358220009742 putative PBP binding regions; other site 358220009743 ABC-ATPase subunit interface; other site 358220009744 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 358220009745 Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct...; Region: YvrC; cd01143 358220009746 putative binding site residues; other site 358220009747 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 358220009748 homotrimer interface [polypeptide binding]; other site 358220009749 Walker A motif; other site 358220009750 GTP binding site [chemical binding]; other site 358220009751 Walker B motif; other site 358220009752 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 358220009753 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cd01983 358220009754 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 358220009755 catalytic triad [active] 358220009756 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 358220009757 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 358220009758 N-terminal plug; other site 358220009759 ligand-binding site [chemical binding]; other site 358220009760 Cell division protein ZapA; Region: ZapA; pfam05164 358220009761 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 358220009762 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220009763 PAS domain; Region: PAS_9; pfam13426 358220009764 putative active site [active] 358220009765 heme pocket [chemical binding]; other site 358220009766 PAS fold; Region: PAS_7; pfam12860 358220009767 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220009768 PAS domain; Region: PAS_9; pfam13426 358220009769 putative active site [active] 358220009770 heme pocket [chemical binding]; other site 358220009771 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220009772 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220009773 metal binding site [ion binding]; metal-binding site 358220009774 active site 358220009775 I-site; other site 358220009776 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220009777 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 358220009778 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220009779 Zn2+ binding site [ion binding]; other site 358220009780 Mg2+ binding site [ion binding]; other site 358220009781 Family description; Region: DsbD_2; pfam13386 358220009782 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 358220009783 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220009784 FeS/SAM binding site; other site 358220009785 HemN C-terminal domain; Region: HemN_C; pfam06969 358220009786 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 358220009787 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220009788 ligand binding site [chemical binding]; other site 358220009789 flexible hinge region; other site 358220009790 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 358220009791 putative switch regulator; other site 358220009792 non-specific DNA interactions [nucleotide binding]; other site 358220009793 DNA binding site [nucleotide binding] 358220009794 sequence specific DNA binding site [nucleotide binding]; other site 358220009795 putative cAMP binding site [chemical binding]; other site 358220009796 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 358220009797 FixH; Region: FixH; pfam05751 358220009798 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 358220009799 4Fe-4S binding domain; Region: Fer4_5; pfam12801 358220009800 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 358220009801 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 358220009802 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 358220009803 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 358220009804 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 358220009805 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 358220009806 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 358220009807 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 358220009808 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 358220009809 Low-spin heme binding site [chemical binding]; other site 358220009810 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 358220009811 Putative water exit pathway; other site 358220009812 Binuclear center (active site) [active] 358220009813 Putative proton exit pathway; other site 358220009814 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 358220009815 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 358220009816 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 358220009817 metal-binding site [ion binding] 358220009818 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 358220009819 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 358220009820 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 358220009821 Ligand Binding Site [chemical binding]; other site 358220009822 malonyl-CoA synthase; Validated; Region: PRK07514 358220009823 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 358220009824 acyl-activating enzyme (AAE) consensus motif; other site 358220009825 active site 358220009826 AMP binding site [chemical binding]; other site 358220009827 CoA binding site [chemical binding]; other site 358220009828 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 358220009829 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220009830 substrate binding site [chemical binding]; other site 358220009831 oxyanion hole (OAH) forming residues; other site 358220009832 trimer interface [polypeptide binding]; other site 358220009833 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220009834 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 358220009835 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220009836 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220009837 DNA-binding site [nucleotide binding]; DNA binding site 358220009838 FCD domain; Region: FCD; pfam07729 358220009839 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220009840 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220009841 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220009842 putative effector binding pocket; other site 358220009843 dimerization interface [polypeptide binding]; other site 358220009844 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220009845 EamA-like transporter family; Region: EamA; pfam00892 358220009846 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 358220009847 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 358220009848 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 358220009849 Cytochrome c; Region: Cytochrom_C; cl11414 358220009850 acetyl-CoA synthetase; Provisional; Region: PRK00174 358220009851 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 358220009852 active site 358220009853 CoA binding site [chemical binding]; other site 358220009854 acyl-activating enzyme (AAE) consensus motif; other site 358220009855 AMP binding site [chemical binding]; other site 358220009856 acetate binding site [chemical binding]; other site 358220009857 hypothetical protein; Provisional; Region: PRK05208 358220009858 Intradiol dioxygenase supgroup. Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. They break the catechol C1-C2 bond and utilize Fe3+, as opposed to the...; Region: intradiol_dioxygenase_like; cd03457 358220009859 putative active site [active] 358220009860 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220009861 dimerization interface [polypeptide binding]; other site 358220009862 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220009863 dimer interface [polypeptide binding]; other site 358220009864 phosphorylation site [posttranslational modification] 358220009865 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220009866 ATP binding site [chemical binding]; other site 358220009867 Mg2+ binding site [ion binding]; other site 358220009868 G-X-G motif; other site 358220009869 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 358220009870 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220009871 active site 358220009872 phosphorylation site [posttranslational modification] 358220009873 intermolecular recognition site; other site 358220009874 dimerization interface [polypeptide binding]; other site 358220009875 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220009876 DNA binding site [nucleotide binding] 358220009877 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 358220009878 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 358220009879 active site 358220009880 DNA binding site [nucleotide binding] 358220009881 Int/Topo IB signature motif; other site 358220009882 catalytic residues [active] 358220009883 fumarate hydratase; Reviewed; Region: fumC; PRK00485 358220009884 Class II fumarases; Region: Fumarase_classII; cd01362 358220009885 active site 358220009886 tetramer interface [polypeptide binding]; other site 358220009887 putative fumarate hydratase; Provisional; Region: PRK15392 358220009888 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 358220009889 Fumarase C-terminus; Region: Fumerase_C; pfam05683 358220009890 glutamate racemase; Provisional; Region: PRK00865 358220009891 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 358220009892 Integrative and conjugative element ICETn4677 358220009893 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220009894 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 358220009895 active site 358220009896 Int/Topo IB signature motif; other site 358220009897 DNA binding site [nucleotide binding] 358220009898 Protein of unknown function (DUF1044); Region: DUF1044; pfam06296 358220009899 Predicted transcriptional regulator [Transcription]; Region: COG2944 358220009900 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220009901 non-specific DNA binding site [nucleotide binding]; other site 358220009902 salt bridge; other site 358220009903 sequence-specific DNA binding site [nucleotide binding]; other site 358220009904 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 358220009905 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea; Region: NTP-PPase_u4; cd11541 358220009906 putative metal binding site [ion binding]; other site 358220009907 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_3; cd10035 358220009908 putative uracil binding site [chemical binding]; other site 358220009909 putative active site [active] 358220009910 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 358220009911 TIR domain; Region: TIR_2; pfam13676 358220009912 hypothetical protein; Reviewed; Region: PRK00024 358220009913 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 358220009914 MPN+ (JAMM) motif; other site 358220009915 Zinc-binding site [ion binding]; other site 358220009916 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 358220009917 Domain of unknown function (DUF932); Region: DUF932; pfam06067 358220009918 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 358220009919 ParB-like nuclease domain; Region: ParBc; pfam02195 358220009920 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220009921 Coenzyme A binding pocket [chemical binding]; other site 358220009922 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 358220009923 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 358220009924 Chromate transporter; Region: Chromate_transp; pfam02417 358220009925 Predicted transcriptional regulators [Transcription]; Region: COG1695 358220009926 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 358220009927 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 358220009928 ArsC family; Region: ArsC; pfam03960 358220009929 catalytic residues [active] 358220009930 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 358220009931 arsenical-resistance protein; Region: acr3; TIGR00832 358220009932 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 358220009933 Low molecular weight phosphatase family; Region: LMWPc; cd00115 358220009934 active site 358220009935 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 358220009936 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220009937 putative metal binding site [ion binding]; other site 358220009938 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220009939 putative DNA binding site [nucleotide binding]; other site 358220009940 putative Zn2+ binding site [ion binding]; other site 358220009941 Uncharacterized conserved protein [Function unknown]; Region: COG5489 358220009942 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220009943 non-specific DNA binding site [nucleotide binding]; other site 358220009944 salt bridge; other site 358220009945 sequence-specific DNA binding site [nucleotide binding]; other site 358220009946 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 358220009947 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 358220009948 Helix-turn-helix domain; Region: HTH_17; cl17695 358220009949 Replication initiator protein A; Region: RPA; pfam10134 358220009950 ParA-like protein; Provisional; Region: PHA02518 358220009951 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 358220009952 P-loop; other site 358220009953 Magnesium ion binding site [ion binding]; other site 358220009954 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 358220009955 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 358220009956 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 358220009957 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 358220009958 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 358220009959 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220009960 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220009961 DNA-binding site [nucleotide binding]; DNA binding site 358220009962 FCD domain; Region: FCD; pfam07729 358220009963 Transposase domain (DUF772); Region: DUF772; pfam05598 358220009964 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 358220009965 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 358220009966 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 358220009967 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 358220009968 acetaldehyde dehydrogenase; Validated; Region: PRK08300 358220009969 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 358220009970 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 358220009971 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 358220009972 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 358220009973 active site 358220009974 catalytic residues [active] 358220009975 metal binding site [ion binding]; metal-binding site 358220009976 DmpG-like communication domain; Region: DmpG_comm; pfam07836 358220009977 BphX-like; Region: BphX; pfam06139 358220009978 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 358220009979 Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO); Region: Rieske_RO_Alpha_BPDO_like; cd03472 358220009980 beta subunit interaction site [polypeptide binding]; other site 358220009981 alpha subunit interaction site [polypeptide binding]; other site 358220009982 iron-sulfur cluster [ion binding]; other site 358220009983 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 358220009984 beta subunit interface [polypeptide binding]; other site 358220009985 alpha subunit interface [polypeptide binding]; other site 358220009986 active site 358220009987 substrate binding site [chemical binding]; other site 358220009988 Fe binding site [ion binding]; other site 358220009989 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 358220009990 inter-subunit interface; other site 358220009991 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 358220009992 [2Fe-2S] cluster binding site [ion binding]; other site 358220009993 cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase; Region: BphB_TodD; TIGR03325 358220009994 cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB)-like, classical (c) SDRs; Region: BphB-like_SDR_c; cd05348 358220009995 NAD binding site [chemical binding]; other site 358220009996 active site 358220009997 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 358220009998 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 358220009999 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 358220010000 active site 358220010001 Fe binding site [ion binding]; other site 358220010002 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 358220010003 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 358220010004 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 358220010005 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 358220010006 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 358220010007 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220010008 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220010009 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220010010 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 358220010011 dimerization interface [polypeptide binding]; other site 358220010012 substrate binding pocket [chemical binding]; other site 358220010013 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 358220010014 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220010015 Walker A motif; other site 358220010016 ATP binding site [chemical binding]; other site 358220010017 Walker B motif; other site 358220010018 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 358220010019 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 358220010020 ATP binding site [chemical binding]; other site 358220010021 Walker A motif; other site 358220010022 hexamer interface [polypeptide binding]; other site 358220010023 Walker B motif; other site 358220010024 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 358220010025 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 358220010026 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 358220010027 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 358220010028 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220010029 Walker A motif; other site 358220010030 ATP binding site [chemical binding]; other site 358220010031 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 358220010032 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 358220010033 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 358220010034 conjugal transfer protein TrbL; Provisional; Region: PRK13875 358220010035 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 358220010036 conjugal transfer protein TrbF; Provisional; Region: PRK13872 358220010037 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 358220010038 VirB7 interaction site; other site 358220010039 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 358220010040 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 358220010041 Uncharacterized conserved small protein [Function unknown]; Region: COG5639 358220010042 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 358220010043 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220010044 Walker A/P-loop; other site 358220010045 ATP binding site [chemical binding]; other site 358220010046 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 358220010047 putative active site [active] 358220010048 putative metal-binding site [ion binding]; other site 358220010049 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 358220010050 Part of AAA domain; Region: AAA_19; pfam13245 358220010051 Integrase core domain; Region: rve; pfam00665 358220010052 Integrase core domain; Region: rve_3; pfam13683 358220010053 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 358220010054 Found in ATP-dependent protease La (LON); Region: LON; smart00464 358220010055 Found in ATP-dependent protease La (LON); Region: LON; smart00464 358220010056 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220010057 Walker A motif; other site 358220010058 ATP binding site [chemical binding]; other site 358220010059 Walker B motif; other site 358220010060 arginine finger; other site 358220010061 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 358220010062 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 358220010063 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 358220010064 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220010065 Walker A motif; other site 358220010066 ATP binding site [chemical binding]; other site 358220010067 Walker B motif; other site 358220010068 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 358220010069 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 358220010070 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 358220010071 oligomer interface [polypeptide binding]; other site 358220010072 active site residues [active] 358220010073 trigger factor; Provisional; Region: tig; PRK01490 358220010074 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 358220010075 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 358220010076 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 358220010077 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 358220010078 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220010079 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220010080 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 358220010081 active site lid residues [active] 358220010082 substrate binding pocket [chemical binding]; other site 358220010083 catalytic residues [active] 358220010084 substrate-Mg2+ binding site; other site 358220010085 aspartate-rich region 1; other site 358220010086 aspartate-rich region 2; other site 358220010087 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 358220010088 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 358220010089 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 358220010090 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 358220010091 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 358220010092 active site lid residues [active] 358220010093 substrate binding pocket [chemical binding]; other site 358220010094 catalytic residues [active] 358220010095 substrate-Mg2+ binding site; other site 358220010096 aspartate-rich region 1; other site 358220010097 aspartate-rich region 2; other site 358220010098 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 358220010099 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220010100 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 358220010101 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220010102 active site 358220010103 phosphorylation site [posttranslational modification] 358220010104 intermolecular recognition site; other site 358220010105 dimerization interface [polypeptide binding]; other site 358220010106 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220010107 DNA binding site [nucleotide binding] 358220010108 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 358220010109 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220010110 dimer interface [polypeptide binding]; other site 358220010111 phosphorylation site [posttranslational modification] 358220010112 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220010113 ATP binding site [chemical binding]; other site 358220010114 Mg2+ binding site [ion binding]; other site 358220010115 G-X-G motif; other site 358220010116 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 358220010117 Bacterial protein of unknown function (DUF925); Region: DUF925; cl01435 358220010118 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 358220010119 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 358220010120 Acid Phosphatase; Region: Acid_PPase; cl17256 358220010121 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220010122 active site 358220010123 motif II; other site 358220010124 Transcriptional regulators [Transcription]; Region: PurR; COG1609 358220010125 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 358220010126 DNA binding site [nucleotide binding] 358220010127 domain linker motif; other site 358220010128 Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR; Region: PBP1_RegR_EndR_KdgR_like; cd06283 358220010129 putative dimerization interface [polypeptide binding]; other site 358220010130 putative ligand binding site [chemical binding]; other site 358220010131 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 358220010132 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 358220010133 dimerization interface [polypeptide binding]; other site 358220010134 ligand binding site [chemical binding]; other site 358220010135 NADP binding site [chemical binding]; other site 358220010136 catalytic site [active] 358220010137 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 358220010138 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 358220010139 substrate binding site [chemical binding]; other site 358220010140 ATP binding site [chemical binding]; other site 358220010141 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 358220010142 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 358220010143 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 358220010144 Walker A/P-loop; other site 358220010145 ATP binding site [chemical binding]; other site 358220010146 Q-loop/lid; other site 358220010147 ABC transporter signature motif; other site 358220010148 Walker B; other site 358220010149 D-loop; other site 358220010150 H-loop/switch region; other site 358220010151 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220010152 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220010153 substrate binding pocket [chemical binding]; other site 358220010154 membrane-bound complex binding site; other site 358220010155 hinge residues; other site 358220010156 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 358220010157 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220010158 dimer interface [polypeptide binding]; other site 358220010159 conserved gate region; other site 358220010160 putative PBP binding loops; other site 358220010161 ABC-ATPase subunit interface; other site 358220010162 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220010163 dimer interface [polypeptide binding]; other site 358220010164 conserved gate region; other site 358220010165 ABC-ATPase subunit interface; other site 358220010166 ferrochelatase; Reviewed; Region: hemH; PRK00035 358220010167 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 358220010168 C-terminal domain interface [polypeptide binding]; other site 358220010169 active site 358220010170 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 358220010171 active site 358220010172 N-terminal domain interface [polypeptide binding]; other site 358220010173 AAA domain; Region: AAA_32; pfam13654 358220010174 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 358220010175 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 358220010176 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220010177 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220010178 Walker A/P-loop; other site 358220010179 ATP binding site [chemical binding]; other site 358220010180 Q-loop/lid; other site 358220010181 ABC transporter signature motif; other site 358220010182 Walker B; other site 358220010183 D-loop; other site 358220010184 H-loop/switch region; other site 358220010185 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220010186 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220010187 Walker A/P-loop; other site 358220010188 ATP binding site [chemical binding]; other site 358220010189 Q-loop/lid; other site 358220010190 ABC transporter signature motif; other site 358220010191 Walker B; other site 358220010192 D-loop; other site 358220010193 H-loop/switch region; other site 358220010194 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220010195 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220010196 TM-ABC transporter signature motif; other site 358220010197 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220010198 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220010199 TM-ABC transporter signature motif; other site 358220010200 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220010201 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 358220010202 putative ligand binding site [chemical binding]; other site 358220010203 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 358220010204 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220010205 substrate binding site [chemical binding]; other site 358220010206 oxyanion hole (OAH) forming residues; other site 358220010207 trimer interface [polypeptide binding]; other site 358220010208 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 358220010209 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220010210 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 358220010211 acyl-activating enzyme (AAE) consensus motif; other site 358220010212 acyl-activating enzyme (AAE) consensus motif; other site 358220010213 putative AMP binding site [chemical binding]; other site 358220010214 putative active site [active] 358220010215 putative CoA binding site [chemical binding]; other site 358220010216 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 358220010217 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220010218 catalytic loop [active] 358220010219 iron binding site [ion binding]; other site 358220010220 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 358220010221 FAD binding domain in molybdopterin dehydrogenase; Region: FAD_binding_5; pfam00941 358220010222 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 358220010223 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 358220010224 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 358220010225 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220010226 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 358220010227 putative hydrophobic ligand binding site [chemical binding]; other site 358220010228 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 358220010229 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220010230 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; cl17722 358220010231 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 358220010232 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 358220010233 conserved cys residue [active] 358220010234 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220010235 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 358220010236 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 358220010237 FMN binding site [chemical binding]; other site 358220010238 active site 358220010239 substrate binding site [chemical binding]; other site 358220010240 catalytic residue [active] 358220010241 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 358220010242 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 358220010243 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220010244 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220010245 Methyltransferase domain; Region: Methyltransf_31; pfam13847 358220010246 S-adenosylmethionine binding site [chemical binding]; other site 358220010247 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220010248 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220010249 LysR substrate binding domain; Region: LysR_substrate; pfam03466 358220010250 dimerization interface [polypeptide binding]; other site 358220010251 Protein of unknown function (DUF2805); Region: DUF2805; pfam10985 358220010252 serine/threonine protein kinase; Provisional; Region: PRK11768 358220010253 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220010254 C factor cell-cell signaling protein; Provisional; Region: PRK09009 358220010255 NAD(P) binding site [chemical binding]; other site 358220010256 active site 358220010257 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 358220010258 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 358220010259 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 358220010260 DNA photolyase; Region: DNA_photolyase; pfam00875 358220010261 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; pfam10013 358220010262 DNA photolyase; Region: DNA_photolyase; pfam00875 358220010263 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 358220010264 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 358220010265 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 358220010266 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 358220010267 Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]; Region: GrxC; COG0695 358220010268 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 358220010269 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220010270 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220010271 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220010272 putative ligand binding site [chemical binding]; other site 358220010273 3HB-oligomer hydrolase (3HBOH); Region: 3HBOH; pfam10605 358220010274 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220010275 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220010276 TM-ABC transporter signature motif; other site 358220010277 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220010278 TM-ABC transporter signature motif; other site 358220010279 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220010280 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220010281 Walker A/P-loop; other site 358220010282 ATP binding site [chemical binding]; other site 358220010283 Q-loop/lid; other site 358220010284 ABC transporter signature motif; other site 358220010285 Walker B; other site 358220010286 D-loop; other site 358220010287 H-loop/switch region; other site 358220010288 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220010289 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220010290 Walker A/P-loop; other site 358220010291 ATP binding site [chemical binding]; other site 358220010292 Q-loop/lid; other site 358220010293 ABC transporter signature motif; other site 358220010294 Walker B; other site 358220010295 D-loop; other site 358220010296 H-loop/switch region; other site 358220010297 esterase, PHB depolymerase family; Region: esterase_phb; TIGR01840 358220010298 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 358220010299 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220010300 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria; Region: PBP1_SBP_like_2; cd06328 358220010301 putative ligand binding site [chemical binding]; other site 358220010302 PAS fold; Region: PAS_4; pfam08448 358220010303 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220010304 putative active site [active] 358220010305 heme pocket [chemical binding]; other site 358220010306 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 358220010307 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220010308 Walker B motif; other site 358220010309 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 358220010310 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; pfam10087 358220010311 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 358220010312 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 358220010313 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 358220010314 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 358220010315 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220010316 active site 358220010317 phosphorylation site [posttranslational modification] 358220010318 intermolecular recognition site; other site 358220010319 dimerization interface [polypeptide binding]; other site 358220010320 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220010321 DNA binding site [nucleotide binding] 358220010322 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 358220010323 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220010324 HAMP domain; Region: HAMP; pfam00672 358220010325 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220010326 dimer interface [polypeptide binding]; other site 358220010327 phosphorylation site [posttranslational modification] 358220010328 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220010329 ATP binding site [chemical binding]; other site 358220010330 Mg2+ binding site [ion binding]; other site 358220010331 G-X-G motif; other site 358220010332 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 358220010333 RNA binding surface [nucleotide binding]; other site 358220010334 N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases...; Region: PP-ATPase; cd01992 358220010335 Ligand Binding Site [chemical binding]; other site 358220010336 TilS substrate binding domain; Region: TilS; pfam09179 358220010337 Cache domain; Region: Cache_1; pfam02743 358220010338 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220010339 dimerization interface [polypeptide binding]; other site 358220010340 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220010341 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220010342 dimer interface [polypeptide binding]; other site 358220010343 putative CheW interface [polypeptide binding]; other site 358220010344 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 358220010345 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 358220010346 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 358220010347 endonuclease III; Region: ENDO3c; smart00478 358220010348 minor groove reading motif; other site 358220010349 helix-hairpin-helix signature motif; other site 358220010350 substrate binding pocket [chemical binding]; other site 358220010351 active site 358220010352 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 358220010353 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 358220010354 active site 358220010355 HIGH motif; other site 358220010356 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 358220010357 KMSKS motif; other site 358220010358 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 358220010359 tRNA binding surface [nucleotide binding]; other site 358220010360 anticodon binding site; other site 358220010361 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 358220010362 binding surface 358220010363 TPR motif; other site 358220010364 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 358220010365 SnoaL-like domain; Region: SnoaL_3; pfam13474 358220010366 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 358220010367 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 358220010368 substrate binding site [chemical binding]; other site 358220010369 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 358220010370 substrate binding site [chemical binding]; other site 358220010371 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 358220010372 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 358220010373 putative active site [active] 358220010374 putative metal binding site [ion binding]; other site 358220010375 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 358220010376 2-oxoacid dehydrogenase subunit E1; Provisional; Region: PRK13012 358220010377 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 358220010378 dimer interface [polypeptide binding]; other site 358220010379 TPP-binding site [chemical binding]; other site 358220010380 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 358220010381 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220010382 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220010383 putative DNA binding site [nucleotide binding]; other site 358220010384 putative Zn2+ binding site [ion binding]; other site 358220010385 AsnC family; Region: AsnC_trans_reg; pfam01037 358220010386 methionine gamma-lyase; Provisional; Region: PRK07503 358220010387 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 358220010388 homodimer interface [polypeptide binding]; other site 358220010389 substrate-cofactor binding pocket; other site 358220010390 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220010391 catalytic residue [active] 358220010392 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220010393 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220010394 putative DNA binding site [nucleotide binding]; other site 358220010395 putative Zn2+ binding site [ion binding]; other site 358220010396 AsnC family; Region: AsnC_trans_reg; pfam01037 358220010397 Predicted esterase [General function prediction only]; Region: COG0400 358220010398 putative hydrolase; Provisional; Region: PRK11460 358220010399 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 358220010400 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 358220010401 putative active site [active] 358220010402 metal binding site [ion binding]; metal-binding site 358220010403 hypothetical protein; Provisional; Region: PRK09256 358220010404 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 358220010405 Dehydroquinase class II; Region: DHquinase_II; pfam01220 358220010406 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 358220010407 trimer interface [polypeptide binding]; other site 358220010408 active site 358220010409 dimer interface [polypeptide binding]; other site 358220010410 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 358220010411 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 358220010412 active site 358220010413 HIGH motif; other site 358220010414 nucleotide binding site [chemical binding]; other site 358220010415 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 358220010416 active site 358220010417 KMSKS motif; other site 358220010418 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 358220010419 Winged helix-turn helix; Region: HTH_29; pfam13551 358220010420 Homeodomain-like domain; Region: HTH_23; cl17451 358220010421 Integrase core domain; Region: rve; pfam00665 358220010422 Integrase core domain; Region: rve_3; pfam13683 358220010423 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 358220010424 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 358220010425 Uncharacterized conserved protein [Function unknown]; Region: COG2361 358220010426 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 358220010427 putative active site [active] 358220010428 Zn binding site [ion binding]; other site 358220010429 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 358220010430 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 358220010431 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 358220010432 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 358220010433 phosphopeptide binding site; other site 358220010434 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; cl01820 358220010435 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 358220010436 putative hydrophobic ligand binding site [chemical binding]; other site 358220010437 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220010438 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220010439 substrate binding pocket [chemical binding]; other site 358220010440 membrane-bound complex binding site; other site 358220010441 hinge residues; other site 358220010442 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 358220010443 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 358220010444 putative active site [active] 358220010445 catalytic site [active] 358220010446 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 358220010447 putative active site [active] 358220010448 catalytic site [active] 358220010449 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 358220010450 Peptidase family M23; Region: Peptidase_M23; pfam01551 358220010451 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 358220010452 pseudouridine synthase; Region: TIGR00093 358220010453 active site 358220010454 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220010455 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 358220010456 C-terminal domain interface [polypeptide binding]; other site 358220010457 GSH binding site (G-site) [chemical binding]; other site 358220010458 dimer interface [polypeptide binding]; other site 358220010459 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 358220010460 N-terminal domain interface [polypeptide binding]; other site 358220010461 dimer interface [polypeptide binding]; other site 358220010462 substrate binding pocket (H-site) [chemical binding]; other site 358220010463 glutathionine S-transferase; Provisional; Region: PRK10542 358220010464 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 358220010465 C-terminal domain interface [polypeptide binding]; other site 358220010466 GSH binding site (G-site) [chemical binding]; other site 358220010467 dimer interface [polypeptide binding]; other site 358220010468 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 358220010469 N-terminal domain interface [polypeptide binding]; other site 358220010470 dimer interface [polypeptide binding]; other site 358220010471 substrate binding pocket (H-site) [chemical binding]; other site 358220010472 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220010473 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220010474 LysR substrate binding domain; Region: LysR_substrate; pfam03466 358220010475 dimerization interface [polypeptide binding]; other site 358220010476 RibD C-terminal domain; Region: RibD_C; cl17279 358220010477 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 358220010478 Staphylococcal nuclease homologues; Region: SNc; smart00318 358220010479 Catalytic site; other site 358220010480 Staphylococcal nuclease homologue; Region: SNase; pfam00565 358220010481 enterobactin exporter EntS; Provisional; Region: PRK10489 358220010482 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 358220010483 Protein of unknown function (DUF1501); Region: DUF1501; pfam07394 358220010484 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 358220010485 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 358220010486 putative metal binding site [ion binding]; other site 358220010487 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 358220010488 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 358220010489 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 358220010490 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 358220010491 active site 358220010492 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 358220010493 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 358220010494 FMN binding site [chemical binding]; other site 358220010495 substrate binding site [chemical binding]; other site 358220010496 putative catalytic residue [active] 358220010497 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220010498 Response regulator receiver domain; Region: Response_reg; pfam00072 358220010499 active site 358220010500 phosphorylation site [posttranslational modification] 358220010501 intermolecular recognition site; other site 358220010502 dimerization interface [polypeptide binding]; other site 358220010503 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220010504 Zn2+ binding site [ion binding]; other site 358220010505 Mg2+ binding site [ion binding]; other site 358220010506 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 358220010507 catalytic core [active] 358220010508 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 358220010509 PAS domain S-box; Region: sensory_box; TIGR00229 358220010510 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220010511 putative active site [active] 358220010512 heme pocket [chemical binding]; other site 358220010513 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220010514 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220010515 dimer interface [polypeptide binding]; other site 358220010516 phosphorylation site [posttranslational modification] 358220010517 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220010518 ATP binding site [chemical binding]; other site 358220010519 Mg2+ binding site [ion binding]; other site 358220010520 G-X-G motif; other site 358220010521 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220010522 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220010523 active site 358220010524 phosphorylation site [posttranslational modification] 358220010525 intermolecular recognition site; other site 358220010526 dimerization interface [polypeptide binding]; other site 358220010527 Response regulator receiver domain; Region: Response_reg; pfam00072 358220010528 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220010529 active site 358220010530 phosphorylation site [posttranslational modification] 358220010531 intermolecular recognition site; other site 358220010532 dimerization interface [polypeptide binding]; other site 358220010533 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220010534 EamA-like transporter family; Region: EamA; pfam00892 358220010535 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 358220010536 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 358220010537 active site 358220010538 Zn binding site [ion binding]; other site 358220010539 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 358220010540 EamA-like transporter family; Region: EamA; pfam00892 358220010541 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220010542 PAS domain; Region: PAS_9; pfam13426 358220010543 putative active site [active] 358220010544 heme pocket [chemical binding]; other site 358220010545 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220010546 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220010547 metal binding site [ion binding]; metal-binding site 358220010548 active site 358220010549 I-site; other site 358220010550 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220010551 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 358220010552 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 358220010553 GTP/Mg2+ binding site [chemical binding]; other site 358220010554 G4 box; other site 358220010555 G5 box; other site 358220010556 G1 box; other site 358220010557 Switch I region; other site 358220010558 G2 box; other site 358220010559 G3 box; other site 358220010560 Switch II region; other site 358220010561 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 358220010562 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl17352 358220010563 (3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs; Region: hydroxyacyl-CoA-like_DH_SDR_c-like; cd05353 358220010564 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 358220010565 NAD binding site [chemical binding]; other site 358220010566 homodimer interface [polypeptide binding]; other site 358220010567 active site 358220010568 Domain of unknown function (DUF427); Region: DUF427; pfam04248 358220010569 Protein of unknown function (DUF938); Region: DUF938; pfam06080 358220010570 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220010571 catalytic loop [active] 358220010572 iron binding site [ion binding]; other site 358220010573 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 358220010574 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 358220010575 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 358220010576 dimerization interface [polypeptide binding]; other site 358220010577 active site 358220010578 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 358220010579 homopentamer interface [polypeptide binding]; other site 358220010580 active site 358220010581 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 358220010582 putative RNA binding site [nucleotide binding]; other site 358220010583 aminotransferase; Validated; Region: PRK07337 358220010584 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220010585 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220010586 homodimer interface [polypeptide binding]; other site 358220010587 catalytic residue [active] 358220010588 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 358220010589 active site 358220010590 TolQ protein; Region: tolQ; TIGR02796 358220010591 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 358220010592 TolR protein; Region: tolR; TIGR02801 358220010593 TolA protein; Region: tolA_full; TIGR02794 358220010594 TonB C terminal; Region: TonB_2; pfam13103 358220010595 metabolite-proton symporter; Region: 2A0106; TIGR00883 358220010596 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220010597 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 358220010598 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 358220010599 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 358220010600 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 358220010601 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 358220010602 D-pathway; other site 358220010603 Putative ubiquinol binding site [chemical binding]; other site 358220010604 Low-spin heme (heme b) binding site [chemical binding]; other site 358220010605 Putative water exit pathway; other site 358220010606 Binuclear center (heme o3/CuB) [ion binding]; other site 358220010607 K-pathway; other site 358220010608 Putative proton exit pathway; other site 358220010609 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 358220010610 Subunit I/III interface [polypeptide binding]; other site 358220010611 Subunit III/IV interface [polypeptide binding]; other site 358220010612 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 358220010613 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 358220010614 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220010615 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 358220010616 dimer interface [polypeptide binding]; other site 358220010617 phosphorylation site [posttranslational modification] 358220010618 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220010619 ATP binding site [chemical binding]; other site 358220010620 Mg2+ binding site [ion binding]; other site 358220010621 G-X-G motif; other site 358220010622 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 358220010623 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220010624 active site 358220010625 phosphorylation site [posttranslational modification] 358220010626 intermolecular recognition site; other site 358220010627 dimerization interface [polypeptide binding]; other site 358220010628 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 358220010629 putative transporter; Reviewed; Region: PRK12369 358220010630 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 358220010631 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 358220010632 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 358220010633 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 358220010634 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 358220010635 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 358220010636 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 358220010637 substrate binding site [chemical binding]; other site 358220010638 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 358220010639 substrate binding site [chemical binding]; other site 358220010640 ligand binding site [chemical binding]; other site 358220010641 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 358220010642 malate dehydrogenase; Provisional; Region: PRK05442 358220010643 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 358220010644 NAD(P) binding site [chemical binding]; other site 358220010645 dimer interface [polypeptide binding]; other site 358220010646 malate binding site [chemical binding]; other site 358220010647 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 358220010648 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220010649 DNA-binding site [nucleotide binding]; DNA binding site 358220010650 UTRA domain; Region: UTRA; pfam07702 358220010651 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 358220010652 Iron-sulfur protein interface; other site 358220010653 proximal quinone binding site [chemical binding]; other site 358220010654 SdhD (CybS) interface [polypeptide binding]; other site 358220010655 proximal heme binding site [chemical binding]; other site 358220010656 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 358220010657 SdhC subunit interface [polypeptide binding]; other site 358220010658 proximal heme binding site [chemical binding]; other site 358220010659 cardiolipin binding site; other site 358220010660 Iron-sulfur protein interface; other site 358220010661 proximal quinone binding site [chemical binding]; other site 358220010662 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 358220010663 L-aspartate oxidase; Provisional; Region: PRK06175 358220010664 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 358220010665 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 358220010666 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 358220010667 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 358220010668 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 358220010669 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 358220010670 dimer interface [polypeptide binding]; other site 358220010671 active site 358220010672 citrylCoA binding site [chemical binding]; other site 358220010673 NADH binding [chemical binding]; other site 358220010674 cationic pore residues; other site 358220010675 oxalacetate/citrate binding site [chemical binding]; other site 358220010676 coenzyme A binding site [chemical binding]; other site 358220010677 catalytic triad [active] 358220010678 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220010679 Homeodomain-like domain; Region: HTH_23; cl17451 358220010680 putative transposase OrfB; Reviewed; Region: PHA02517 358220010681 Integrase core domain; Region: rve; pfam00665 358220010682 Integrase core domain; Region: rve_3; pfam13683 358220010683 Cupin; Region: Cupin_6; pfam12852 358220010684 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220010685 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 358220010686 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 358220010687 NADP binding site [chemical binding]; other site 358220010688 active site 358220010689 steroid binding site; other site 358220010690 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 358220010691 putative metal binding site [ion binding]; other site 358220010692 putative homodimer interface [polypeptide binding]; other site 358220010693 putative homotetramer interface [polypeptide binding]; other site 358220010694 putative homodimer-homodimer interface [polypeptide binding]; other site 358220010695 putative allosteric switch controlling residues; other site 358220010696 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 358220010697 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 358220010698 substrate binding site [chemical binding]; other site 358220010699 catalytic Zn binding site [ion binding]; other site 358220010700 NAD binding site [chemical binding]; other site 358220010701 structural Zn binding site [ion binding]; other site 358220010702 dimer interface [polypeptide binding]; other site 358220010703 S-formylglutathione hydrolase; Region: PLN02442 358220010704 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 358220010705 putative metal dependent hydrolase; Provisional; Region: PRK11598 358220010706 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 358220010707 Sulfatase; Region: Sulfatase; pfam00884 358220010708 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 358220010709 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 358220010710 NAD(P) binding site [chemical binding]; other site 358220010711 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220010712 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220010713 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220010714 dimerization interface [polypeptide binding]; other site 358220010715 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220010716 Coenzyme A binding pocket [chemical binding]; other site 358220010717 Radical SAM superfamily; Region: Radical_SAM; pfam04055 358220010718 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 358220010719 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 358220010720 DNA binding site [nucleotide binding] 358220010721 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220010722 non-specific DNA binding site [nucleotide binding]; other site 358220010723 salt bridge; other site 358220010724 sequence-specific DNA binding site [nucleotide binding]; other site 358220010725 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220010726 non-specific DNA binding site [nucleotide binding]; other site 358220010727 salt bridge; other site 358220010728 sequence-specific DNA binding site [nucleotide binding]; other site 358220010729 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220010730 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220010731 DNA-binding site [nucleotide binding]; DNA binding site 358220010732 FCD domain; Region: FCD; pfam07729 358220010733 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 358220010734 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 358220010735 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220010736 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 358220010737 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_5; cd07823 358220010738 putative hydrophobic ligand binding site [chemical binding]; other site 358220010739 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 358220010740 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 358220010741 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 358220010742 hypothetical protein; Provisional; Region: PRK08296 358220010743 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 358220010744 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220010745 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_5; cd06338 358220010746 putative ligand binding site [chemical binding]; other site 358220010747 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220010748 TM-ABC transporter signature motif; other site 358220010749 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220010750 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220010751 TM-ABC transporter signature motif; other site 358220010752 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220010753 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220010754 Walker A/P-loop; other site 358220010755 ATP binding site [chemical binding]; other site 358220010756 Q-loop/lid; other site 358220010757 ABC transporter signature motif; other site 358220010758 Walker B; other site 358220010759 D-loop; other site 358220010760 H-loop/switch region; other site 358220010761 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220010762 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220010763 Walker A/P-loop; other site 358220010764 ATP binding site [chemical binding]; other site 358220010765 Q-loop/lid; other site 358220010766 ABC transporter signature motif; other site 358220010767 Walker B; other site 358220010768 D-loop; other site 358220010769 H-loop/switch region; other site 358220010770 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 358220010771 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220010772 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 358220010773 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 358220010774 Isochorismatase family; Region: Isochorismatase; pfam00857 358220010775 catalytic triad [active] 358220010776 conserved cis-peptide bond; other site 358220010777 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220010778 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 358220010779 Argininosuccinate lyase [Amino acid transport and metabolism]; Region: ArgH; COG0165 358220010780 active sites [active] 358220010781 tetramer interface [polypeptide binding]; other site 358220010782 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220010783 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 358220010784 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220010785 dimerization interface [polypeptide binding]; other site 358220010786 Transposase domain (DUF772); Region: DUF772; pfam05598 358220010787 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 358220010788 DDE superfamily endonuclease; Region: DDE_4; cl17710 358220010789 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 358220010790 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 358220010791 PLD-like domain; Region: PLDc_2; pfam13091 358220010792 putative active site [active] 358220010793 catalytic site [active] 358220010794 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 358220010795 PLD-like domain; Region: PLDc_2; pfam13091 358220010796 putative active site [active] 358220010797 catalytic site [active] 358220010798 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 358220010799 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 358220010800 FMN binding site [chemical binding]; other site 358220010801 active site 358220010802 catalytic residues [active] 358220010803 substrate binding site [chemical binding]; other site 358220010804 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 358220010805 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220010806 S-adenosylmethionine binding site [chemical binding]; other site 358220010807 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 358220010808 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220010809 Coenzyme A binding pocket [chemical binding]; other site 358220010810 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220010811 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220010812 active site 358220010813 phosphorylation site [posttranslational modification] 358220010814 intermolecular recognition site; other site 358220010815 dimerization interface [polypeptide binding]; other site 358220010816 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220010817 DNA binding residues [nucleotide binding] 358220010818 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220010819 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220010820 dimer interface [polypeptide binding]; other site 358220010821 phosphorylation site [posttranslational modification] 358220010822 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220010823 ATP binding site [chemical binding]; other site 358220010824 Mg2+ binding site [ion binding]; other site 358220010825 G-X-G motif; other site 358220010826 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220010827 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220010828 active site 358220010829 phosphorylation site [posttranslational modification] 358220010830 intermolecular recognition site; other site 358220010831 dimerization interface [polypeptide binding]; other site 358220010832 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 358220010833 NAD(P) binding site [chemical binding]; other site 358220010834 catalytic residues [active] 358220010835 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 358220010836 Clp amino terminal domain; Region: Clp_N; pfam02861 358220010837 Clp amino terminal domain; Region: Clp_N; pfam02861 358220010838 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220010839 Walker A motif; other site 358220010840 ATP binding site [chemical binding]; other site 358220010841 Walker B motif; other site 358220010842 arginine finger; other site 358220010843 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220010844 Walker A motif; other site 358220010845 ATP binding site [chemical binding]; other site 358220010846 Walker B motif; other site 358220010847 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 358220010848 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 358220010849 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220010850 non-specific DNA binding site [nucleotide binding]; other site 358220010851 salt bridge; other site 358220010852 sequence-specific DNA binding site [nucleotide binding]; other site 358220010853 Integrase core domain; Region: rve; pfam00665 358220010854 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 358220010855 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220010856 Walker A motif; other site 358220010857 ATP binding site [chemical binding]; other site 358220010858 Walker B motif; other site 358220010859 arginine finger; other site 358220010860 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 358220010861 Type II transport protein GspH; Region: GspH; pfam12019 358220010862 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 358220010863 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 358220010864 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 358220010865 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 358220010866 PilX N-terminal; Region: PilX_N; pfam14341 358220010867 Type IV pilus assembly protein PilX C-term; Region: PilX; pfam13681 358220010868 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 358220010869 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 358220010870 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 358220010871 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 358220010872 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 358220010873 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220010874 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 358220010875 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 358220010876 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 358220010877 FMN binding site [chemical binding]; other site 358220010878 substrate binding site [chemical binding]; other site 358220010879 putative catalytic residue [active] 358220010880 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 358220010881 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 358220010882 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220010883 active site 358220010884 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 358220010885 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 358220010886 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 358220010887 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 358220010888 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 358220010889 Ligand binding site [chemical binding]; other site 358220010890 Electron transfer flavoprotein domain; Region: ETF; pfam01012 358220010891 Mechanosensitive ion channel; Region: MS_channel; pfam00924 358220010892 enoyl-CoA hydratase; Validated; Region: PRK08139 358220010893 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220010894 substrate binding site [chemical binding]; other site 358220010895 oxyanion hole (OAH) forming residues; other site 358220010896 trimer interface [polypeptide binding]; other site 358220010897 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 358220010898 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 358220010899 putative active site [active] 358220010900 Zn binding site [ion binding]; other site 358220010901 MoxR-like ATPases [General function prediction only]; Region: COG0714 358220010902 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220010903 Walker A motif; other site 358220010904 ATP binding site [chemical binding]; other site 358220010905 Walker B motif; other site 358220010906 arginine finger; other site 358220010907 Protein of unknown function DUF58; Region: DUF58; pfam01882 358220010908 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 358220010909 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 358220010910 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 358220010911 Transglycosylase SLT domain; Region: SLT_2; pfam13406 358220010912 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 358220010913 N-acetyl-D-glucosamine binding site [chemical binding]; other site 358220010914 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 358220010915 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 358220010916 Walker A/P-loop; other site 358220010917 ATP binding site [chemical binding]; other site 358220010918 Q-loop/lid; other site 358220010919 ABC transporter signature motif; other site 358220010920 Walker B; other site 358220010921 D-loop; other site 358220010922 H-loop/switch region; other site 358220010923 ABC-2 type transporter; Region: ABC2_membrane; cl17235 358220010924 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 358220010925 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220010926 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 358220010927 putative ligand binding site [chemical binding]; other site 358220010928 This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa; Region: ACD_sHsps_p23-like; cd00298 358220010929 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 358220010930 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 358220010931 FtsX-like permease family; Region: FtsX; pfam02687 358220010932 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 358220010933 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 358220010934 Walker A/P-loop; other site 358220010935 ATP binding site [chemical binding]; other site 358220010936 Q-loop/lid; other site 358220010937 ABC transporter signature motif; other site 358220010938 Walker B; other site 358220010939 D-loop; other site 358220010940 H-loop/switch region; other site 358220010941 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 358220010942 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220010943 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 358220010944 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 358220010945 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220010946 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220010947 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_5; cd06338 358220010948 putative ligand binding site [chemical binding]; other site 358220010949 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220010950 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220010951 TM-ABC transporter signature motif; other site 358220010952 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220010953 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220010954 TM-ABC transporter signature motif; other site 358220010955 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220010956 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220010957 Walker A/P-loop; other site 358220010958 ATP binding site [chemical binding]; other site 358220010959 Q-loop/lid; other site 358220010960 ABC transporter signature motif; other site 358220010961 Walker B; other site 358220010962 D-loop; other site 358220010963 H-loop/switch region; other site 358220010964 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220010965 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220010966 Walker A/P-loop; other site 358220010967 ATP binding site [chemical binding]; other site 358220010968 Q-loop/lid; other site 358220010969 ABC transporter signature motif; other site 358220010970 Walker B; other site 358220010971 D-loop; other site 358220010972 H-loop/switch region; other site 358220010973 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 358220010974 Salicylaldehyde dehydrogenase, DoxF-like; Region: ALDH_SaliADH; cd07105 358220010975 NAD(P) binding site [chemical binding]; other site 358220010976 catalytic residues [active] 358220010977 UGMP family protein; Validated; Region: PRK09604 358220010978 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 358220010979 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220010980 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 358220010981 dimerization interface [polypeptide binding]; other site 358220010982 ligand binding site [chemical binding]; other site 358220010983 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 358220010984 ANTAR domain; Region: ANTAR; pfam03861 358220010985 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 358220010986 NMT1-like family; Region: NMT1_2; pfam13379 358220010987 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 358220010988 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220010989 dimer interface [polypeptide binding]; other site 358220010990 conserved gate region; other site 358220010991 putative PBP binding loops; other site 358220010992 ABC-ATPase subunit interface; other site 358220010993 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 358220010994 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 358220010995 Walker A/P-loop; other site 358220010996 ATP binding site [chemical binding]; other site 358220010997 Q-loop/lid; other site 358220010998 ABC transporter signature motif; other site 358220010999 Walker B; other site 358220011000 D-loop; other site 358220011001 H-loop/switch region; other site 358220011002 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 358220011003 FOG: CBS domain [General function prediction only]; Region: COG0517 358220011004 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220011005 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 358220011006 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 358220011007 DctM-like transporters; Region: DctM; pfam06808 358220011008 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 358220011009 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 358220011010 AAA domain; Region: AAA_33; pfam13671 358220011011 ATP-binding site [chemical binding]; other site 358220011012 Gluconate-6-phosphate binding site [chemical binding]; other site 358220011013 Transcriptional regulators [Transcription]; Region: PurR; COG1609 358220011014 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 358220011015 DNA binding site [nucleotide binding] 358220011016 domain linker motif; other site 358220011017 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 358220011018 putative ligand binding site [chemical binding]; other site 358220011019 putative dimerization interface [polypeptide binding]; other site 358220011020 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011021 PAS domain; Region: PAS_9; pfam13426 358220011022 putative active site [active] 358220011023 heme pocket [chemical binding]; other site 358220011024 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 358220011025 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220011026 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220011027 dimer interface [polypeptide binding]; other site 358220011028 putative CheW interface [polypeptide binding]; other site 358220011029 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 358220011030 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220011031 putative substrate translocation pore; other site 358220011032 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 358220011033 active site 358220011034 Protein phosphatase 2C; Region: PP2C; pfam00481 358220011035 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 358220011036 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 358220011037 active site 358220011038 ATP binding site [chemical binding]; other site 358220011039 substrate binding site [chemical binding]; other site 358220011040 activation loop (A-loop); other site 358220011041 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 358220011042 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220011043 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 358220011044 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 358220011045 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 358220011046 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 358220011047 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 358220011048 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 358220011049 [2Fe-2S] cluster binding site [ion binding]; other site 358220011050 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 358220011051 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 358220011052 [4Fe-4S] binding site [ion binding]; other site 358220011053 molybdopterin cofactor binding site; other site 358220011054 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 358220011055 molybdopterin cofactor binding site; other site 358220011056 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 358220011057 glycosyl transferase family protein; Provisional; Region: PRK08136 358220011058 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 358220011059 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 358220011060 active site 358220011061 SAM binding site [chemical binding]; other site 358220011062 homodimer interface [polypeptide binding]; other site 358220011063 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220011064 putative CheW interface [polypeptide binding]; other site 358220011065 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 358220011066 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 358220011067 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 358220011068 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 358220011069 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220011070 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220011071 putative ligand binding site [chemical binding]; other site 358220011072 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 358220011073 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 358220011074 N-terminal plug; other site 358220011075 ligand-binding site [chemical binding]; other site 358220011076 HI0933-like protein; Region: HI0933_like; pfam03486 358220011077 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 358220011078 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220011079 dimerization interface [polypeptide binding]; other site 358220011080 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011081 PAS domain; Region: PAS_9; pfam13426 358220011082 putative active site [active] 358220011083 heme pocket [chemical binding]; other site 358220011084 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220011085 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220011086 metal binding site [ion binding]; metal-binding site 358220011087 active site 358220011088 I-site; other site 358220011089 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220011090 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 358220011091 Yqey-like protein; Region: YqeY; pfam09424 358220011092 transcriptional activator TtdR; Provisional; Region: PRK09801 358220011093 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220011094 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 358220011095 putative effector binding pocket; other site 358220011096 putative dimerization interface [polypeptide binding]; other site 358220011097 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 358220011098 tartrate dehydrogenase; Region: TTC; TIGR02089 358220011099 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220011100 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220011101 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220011102 dimerization interface [polypeptide binding]; other site 358220011103 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220011104 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_16; cd07263 358220011105 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 358220011106 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220011107 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220011108 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220011109 NADH(P)-binding; Region: NAD_binding_10; pfam13460 358220011110 NAD(P) binding site [chemical binding]; other site 358220011111 active site 358220011112 peptidase PmbA; Provisional; Region: PRK11040 358220011113 Protein of unknown function (DUF615); Region: DUF615; pfam04751 358220011114 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 358220011115 MPT binding site; other site 358220011116 trimer interface [polypeptide binding]; other site 358220011117 serine O-acetyltransferase; Region: cysE; TIGR01172 358220011118 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 358220011119 trimer interface [polypeptide binding]; other site 358220011120 active site 358220011121 substrate binding site [chemical binding]; other site 358220011122 CoA binding site [chemical binding]; other site 358220011123 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 358220011124 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 358220011125 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 358220011126 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 358220011127 active site 358220011128 dimerization interface [polypeptide binding]; other site 358220011129 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 358220011130 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011131 active site 358220011132 phosphorylation site [posttranslational modification] 358220011133 intermolecular recognition site; other site 358220011134 dimerization interface [polypeptide binding]; other site 358220011135 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220011136 Zn2+ binding site [ion binding]; other site 358220011137 Mg2+ binding site [ion binding]; other site 358220011138 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011139 PAS domain; Region: PAS_9; pfam13426 358220011140 putative active site [active] 358220011141 heme pocket [chemical binding]; other site 358220011142 PAS domain; Region: PAS_9; pfam13426 358220011143 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011144 PAS fold; Region: PAS_3; pfam08447 358220011145 putative active site [active] 358220011146 heme pocket [chemical binding]; other site 358220011147 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 358220011148 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011149 putative active site [active] 358220011150 heme pocket [chemical binding]; other site 358220011151 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220011152 dimer interface [polypeptide binding]; other site 358220011153 phosphorylation site [posttranslational modification] 358220011154 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220011155 ATP binding site [chemical binding]; other site 358220011156 Mg2+ binding site [ion binding]; other site 358220011157 G-X-G motif; other site 358220011158 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220011159 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011160 active site 358220011161 phosphorylation site [posttranslational modification] 358220011162 intermolecular recognition site; other site 358220011163 dimerization interface [polypeptide binding]; other site 358220011164 Response regulator receiver domain; Region: Response_reg; pfam00072 358220011165 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011166 active site 358220011167 phosphorylation site [posttranslational modification] 358220011168 intermolecular recognition site; other site 358220011169 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 358220011170 putative binding surface; other site 358220011171 active site 358220011172 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220011173 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011174 putative active site [active] 358220011175 heme pocket [chemical binding]; other site 358220011176 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011177 putative active site [active] 358220011178 heme pocket [chemical binding]; other site 358220011179 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220011180 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220011181 metal binding site [ion binding]; metal-binding site 358220011182 active site 358220011183 I-site; other site 358220011184 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220011185 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 358220011186 MutS domain I; Region: MutS_I; pfam01624 358220011187 MutS domain II; Region: MutS_II; pfam05188 358220011188 MutS domain III; Region: MutS_III; pfam05192 358220011189 MutS domain V; Region: MutS_V; pfam00488 358220011190 Walker A/P-loop; other site 358220011191 ATP binding site [chemical binding]; other site 358220011192 Q-loop/lid; other site 358220011193 ABC transporter signature motif; other site 358220011194 Walker B; other site 358220011195 D-loop; other site 358220011196 H-loop/switch region; other site 358220011197 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 358220011198 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 358220011199 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220011200 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 358220011201 Protein of unknown function (DUF422); Region: DUF422; cl00991 358220011202 Uncharacterized protein conserved in bacteria (DUF2236); Region: DUF2236; cl01472 358220011203 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 358220011204 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 358220011205 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220011206 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220011207 metal binding site [ion binding]; metal-binding site 358220011208 active site 358220011209 I-site; other site 358220011210 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 358220011211 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 358220011212 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220011213 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220011214 metal binding site [ion binding]; metal-binding site 358220011215 active site 358220011216 I-site; other site 358220011217 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 358220011218 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 358220011219 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220011220 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220011221 metal binding site [ion binding]; metal-binding site 358220011222 active site 358220011223 I-site; other site 358220011224 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 358220011225 FAD binding domain; Region: FAD_binding_4; pfam01565 358220011226 Berberine and berberine like; Region: BBE; pfam08031 358220011227 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220011228 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011229 putative active site [active] 358220011230 heme pocket [chemical binding]; other site 358220011231 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011232 putative active site [active] 358220011233 heme pocket [chemical binding]; other site 358220011234 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220011235 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220011236 metal binding site [ion binding]; metal-binding site 358220011237 active site 358220011238 I-site; other site 358220011239 MltA-interacting protein MipA; Region: MipA; cl01504 358220011240 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 358220011241 Predicted membrane protein (DUF2306); Region: DUF2306; pfam10067 358220011242 2TM domain; Region: 2TM; pfam13239 358220011243 Predicted dienelactone hydrolase [General function prediction only]; Region: COG4188 358220011244 2TM domain; Region: 2TM; pfam13239 358220011245 Histidine kinase; Region: His_kinase; pfam06580 358220011246 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 358220011247 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011248 active site 358220011249 phosphorylation site [posttranslational modification] 358220011250 intermolecular recognition site; other site 358220011251 dimerization interface [polypeptide binding]; other site 358220011252 LytTr DNA-binding domain; Region: LytTR; smart00850 358220011253 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 358220011254 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 358220011255 Protein export membrane protein; Region: SecD_SecF; cl14618 358220011256 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 358220011257 Protein export membrane protein; Region: SecD_SecF; cl14618 358220011258 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 358220011259 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 358220011260 carboxyltransferase (CT) interaction site; other site 358220011261 biotinylation site [posttranslational modification]; other site 358220011262 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220011263 LysE type translocator; Region: LysE; cl00565 358220011264 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220011265 Walker A/P-loop; other site 358220011266 ATP binding site [chemical binding]; other site 358220011267 ABC transporter; Region: ABC_tran; pfam00005 358220011268 Q-loop/lid; other site 358220011269 ABC transporter signature motif; other site 358220011270 Walker B; other site 358220011271 D-loop; other site 358220011272 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 358220011273 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 358220011274 UDP-glucose 4 epimerase (G4E), subgroup 3, extended (e) SDRs; Region: UDP_G4E_3_SDR_e; cd05240 358220011275 putative NAD(P) binding site [chemical binding]; other site 358220011276 active site 358220011277 putative substrate binding site [chemical binding]; other site 358220011278 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 358220011279 Sodium Bile acid symporter family; Region: SBF; pfam01758 358220011280 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 358220011281 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 358220011282 short chain dehydrogenase; Provisional; Region: PRK07024 358220011283 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220011284 NAD(P) binding site [chemical binding]; other site 358220011285 active site 358220011286 Transcriptional regulator [Transcription]; Region: IclR; COG1414 358220011287 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 358220011288 Bacterial transcriptional regulator; Region: IclR; pfam01614 358220011289 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 358220011290 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 358220011291 catalytic core [active] 358220011292 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011293 PAS domain; Region: PAS_9; pfam13426 358220011294 putative active site [active] 358220011295 heme pocket [chemical binding]; other site 358220011296 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011297 PAS domain; Region: PAS_9; pfam13426 358220011298 putative active site [active] 358220011299 heme pocket [chemical binding]; other site 358220011300 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220011301 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220011302 dimer interface [polypeptide binding]; other site 358220011303 phosphorylation site [posttranslational modification] 358220011304 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220011305 ATP binding site [chemical binding]; other site 358220011306 Mg2+ binding site [ion binding]; other site 358220011307 G-X-G motif; other site 358220011308 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 358220011309 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 358220011310 substrate binding pocket [chemical binding]; other site 358220011311 membrane-bound complex binding site; other site 358220011312 hinge residues; other site 358220011313 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220011314 Zn2+ binding site [ion binding]; other site 358220011315 Mg2+ binding site [ion binding]; other site 358220011316 Response regulator receiver domain; Region: Response_reg; pfam00072 358220011317 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011318 active site 358220011319 phosphorylation site [posttranslational modification] 358220011320 intermolecular recognition site; other site 358220011321 dimerization interface [polypeptide binding]; other site 358220011322 Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Region: HTH_MerR-trunc; cd04762 358220011323 DNA binding residues [nucleotide binding] 358220011324 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220011325 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011326 active site 358220011327 phosphorylation site [posttranslational modification] 358220011328 intermolecular recognition site; other site 358220011329 dimerization interface [polypeptide binding]; other site 358220011330 Response regulator receiver domain; Region: Response_reg; pfam00072 358220011331 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011332 active site 358220011333 phosphorylation site [posttranslational modification] 358220011334 intermolecular recognition site; other site 358220011335 dimerization interface [polypeptide binding]; other site 358220011336 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 358220011337 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 358220011338 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220011339 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 358220011340 putative C-terminal domain interface [polypeptide binding]; other site 358220011341 putative GSH binding site (G-site) [chemical binding]; other site 358220011342 putative dimer interface [polypeptide binding]; other site 358220011343 C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases; Region: GST_C_GTT1_like; cd03189 358220011344 putative N-terminal domain interface [polypeptide binding]; other site 358220011345 putative dimer interface [polypeptide binding]; other site 358220011346 putative substrate binding pocket (H-site) [chemical binding]; other site 358220011347 Low molecular weight phosphatase family; Region: LMWPc; cd00115 358220011348 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 358220011349 active site 358220011350 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 358220011351 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 358220011352 XdhC Rossmann domain; Region: XdhC_C; pfam13478 358220011353 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 358220011354 putative hydrophobic ligand binding site [chemical binding]; other site 358220011355 Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: CoxE; COG3552 358220011356 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 358220011357 metal ion-dependent adhesion site (MIDAS); other site 358220011358 MoxR-like ATPases [General function prediction only]; Region: COG0714 358220011359 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220011360 Walker A motif; other site 358220011361 ATP binding site [chemical binding]; other site 358220011362 Walker B motif; other site 358220011363 arginine finger; other site 358220011364 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 358220011365 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 358220011366 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 358220011367 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 358220011368 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220011369 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 358220011370 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220011371 catalytic loop [active] 358220011372 iron binding site [ion binding]; other site 358220011373 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 358220011374 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 358220011375 DNA-binding interface [nucleotide binding]; DNA binding site 358220011376 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 358220011377 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg6; cd04781 358220011378 DNA binding residues [nucleotide binding] 358220011379 putative dimer interface [polypeptide binding]; other site 358220011380 putative metal binding residues [ion binding]; other site 358220011381 Protein of unknown function (DUF2938); Region: DUF2938; pfam11158 358220011382 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 358220011383 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 358220011384 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 358220011385 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 358220011386 arsenical-resistance protein; Region: acr3; TIGR00832 358220011387 Low molecular weight phosphatase family; Region: LMWPc; cd00115 358220011388 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 358220011389 active site 358220011390 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 358220011391 putative metal binding site [ion binding]; other site 358220011392 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220011393 putative DNA binding site [nucleotide binding]; other site 358220011394 putative Zn2+ binding site [ion binding]; other site 358220011395 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220011396 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 358220011397 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 358220011398 hydrophobic ligand binding site; other site 358220011399 DoxX-like family; Region: DoxX_3; pfam13781 358220011400 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 358220011401 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 358220011402 ABC1 family; Region: ABC1; cl17513 358220011403 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 358220011404 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 358220011405 PBP superfamily domain; Region: PBP_like_2; pfam12849 358220011406 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 358220011407 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 358220011408 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 358220011409 Walker A/P-loop; other site 358220011410 ATP binding site [chemical binding]; other site 358220011411 Q-loop/lid; other site 358220011412 ABC transporter signature motif; other site 358220011413 Walker B; other site 358220011414 D-loop; other site 358220011415 H-loop/switch region; other site 358220011416 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 358220011417 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 358220011418 PBP superfamily domain; Region: PBP_like; pfam12727 358220011419 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 358220011420 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 358220011421 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 358220011422 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220011423 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 358220011424 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 358220011425 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 358220011426 TPP-binding site; other site 358220011427 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 358220011428 PYR/PP interface [polypeptide binding]; other site 358220011429 dimer interface [polypeptide binding]; other site 358220011430 TPP binding site [chemical binding]; other site 358220011431 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 358220011432 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 358220011433 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 358220011434 substrate binding pocket [chemical binding]; other site 358220011435 chain length determination region; other site 358220011436 substrate-Mg2+ binding site; other site 358220011437 catalytic residues [active] 358220011438 aspartate-rich region 1; other site 358220011439 active site lid residues [active] 358220011440 aspartate-rich region 2; other site 358220011441 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 358220011442 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 358220011443 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 358220011444 [2Fe-2S] cluster binding site [ion binding]; other site 358220011445 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 358220011446 alpha subunit interface [polypeptide binding]; other site 358220011447 active site 358220011448 substrate binding site [chemical binding]; other site 358220011449 Fe binding site [ion binding]; other site 358220011450 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 358220011451 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 358220011452 active site residue [active] 358220011453 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 358220011454 active site residue [active] 358220011455 Flagellar transcriptional activator (FlhD); Region: FlhD; pfam05247 358220011456 transcriptional activator FlhC; Provisional; Region: PRK12722 358220011457 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 358220011458 Phage virion morphogenesis family; Region: Phage_tail_S; pfam05069 358220011459 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 358220011460 Protein of unknown function (DUF935); Region: DUF935; pfam06074 358220011461 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 358220011462 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 358220011463 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 358220011464 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 358220011465 catalytic residue [active] 358220011466 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 358220011467 active site 358220011468 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220011469 non-specific DNA binding site [nucleotide binding]; other site 358220011470 salt bridge; other site 358220011471 sequence-specific DNA binding site [nucleotide binding]; other site 358220011472 phage-associated protein, BcepMu gp16 family; Region: BcepMu_gp16; TIGR04111 358220011473 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 358220011474 Protein of unknown function (DUF3102); Region: DUF3102; pfam11300 358220011475 Integrase core domain; Region: rve; pfam00665 358220011476 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 358220011477 AAA ATPase domain; Region: AAA_16; pfam13191 358220011478 recombination associated protein; Reviewed; Region: rdgC; PRK00321 358220011479 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 358220011480 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl17257 358220011481 DNA binding residues [nucleotide binding] 358220011482 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 358220011483 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 358220011484 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 358220011485 Phage related hypothetical protein (DUF1799); Region: DUF1799; pfam08809 358220011486 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 358220011487 Phage-related minor tail protein [Function unknown]; Region: COG5281 358220011488 Mu-like prophage protein Com; Region: Mu-like_Com; cl11540 358220011489 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 358220011490 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 358220011491 Domain of unknown function DUF20; Region: UPF0118; pfam01594 358220011492 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 358220011493 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 358220011494 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 358220011495 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 358220011496 domain interfaces; other site 358220011497 active site 358220011498 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 358220011499 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 358220011500 active site 358220011501 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 358220011502 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 358220011503 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 358220011504 YceI-like domain; Region: YceI; smart00867 358220011505 Uncharacterized conserved protein [Function unknown]; Region: COG2353 358220011506 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220011507 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 358220011508 Zn binding site [ion binding]; other site 358220011509 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 358220011510 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 358220011511 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 358220011512 active site 358220011513 HIGH motif; other site 358220011514 nucleotide binding site [chemical binding]; other site 358220011515 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 358220011516 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 358220011517 active site 358220011518 KMSKS motif; other site 358220011519 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 358220011520 tRNA binding surface [nucleotide binding]; other site 358220011521 anticodon binding site; other site 358220011522 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 358220011523 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 358220011524 active site 358220011525 tetramer interface; other site 358220011526 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 358220011527 CPxP motif; other site 358220011528 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 358220011529 nudix motif; other site 358220011530 cysteine synthase B; Region: cysM; TIGR01138 358220011531 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 358220011532 dimer interface [polypeptide binding]; other site 358220011533 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220011534 catalytic residue [active] 358220011535 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220011536 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220011537 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220011538 dimerization interface [polypeptide binding]; other site 358220011539 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 358220011540 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220011541 FAD binding site [chemical binding]; other site 358220011542 substrate binding pocket [chemical binding]; other site 358220011543 catalytic base [active] 358220011544 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 358220011545 CoA-transferase family III; Region: CoA_transf_3; pfam02515 358220011546 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220011547 dimerization interface [polypeptide binding]; other site 358220011548 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220011549 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220011550 dimer interface [polypeptide binding]; other site 358220011551 putative CheW interface [polypeptide binding]; other site 358220011552 riboflavin synthase subunit beta; Provisional; Region: PRK12419 358220011553 active site 358220011554 homopentamer interface [polypeptide binding]; other site 358220011555 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 358220011556 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220011557 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220011558 dimerization interface [polypeptide binding]; other site 358220011559 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220011560 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 358220011561 dihydroxy-acid dehydratase; Provisional; Region: PRK13017 358220011562 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 358220011563 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 358220011564 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 358220011565 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 358220011566 DctM-like transporters; Region: DctM; pfam06808 358220011567 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 358220011568 NADH(P)-binding; Region: NAD_binding_10; pfam13460 358220011569 NAD binding site [chemical binding]; other site 358220011570 substrate binding site [chemical binding]; other site 358220011571 putative active site [active] 358220011572 transcriptional regulator; Provisional; Region: PRK10632 358220011573 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220011574 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220011575 putative effector binding pocket; other site 358220011576 dimerization interface [polypeptide binding]; other site 358220011577 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 358220011578 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 358220011579 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220011580 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011581 active site 358220011582 phosphorylation site [posttranslational modification] 358220011583 intermolecular recognition site; other site 358220011584 dimerization interface [polypeptide binding]; other site 358220011585 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 358220011586 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220011587 NADH(P)-binding; Region: NAD_binding_10; pfam13460 358220011588 NAD(P) binding site [chemical binding]; other site 358220011589 active site 358220011590 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 358220011591 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220011592 catalytic loop [active] 358220011593 iron binding site [ion binding]; other site 358220011594 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 358220011595 FAD binding pocket [chemical binding]; other site 358220011596 FAD binding motif [chemical binding]; other site 358220011597 phosphate binding motif [ion binding]; other site 358220011598 beta-alpha-beta structure motif; other site 358220011599 NAD binding pocket [chemical binding]; other site 358220011600 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 358220011601 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011602 PAS domain; Region: PAS_9; pfam13426 358220011603 putative active site [active] 358220011604 heme pocket [chemical binding]; other site 358220011605 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220011606 ATP binding site [chemical binding]; other site 358220011607 Mg2+ binding site [ion binding]; other site 358220011608 G-X-G motif; other site 358220011609 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 358220011610 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011611 active site 358220011612 phosphorylation site [posttranslational modification] 358220011613 intermolecular recognition site; other site 358220011614 dimerization interface [polypeptide binding]; other site 358220011615 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220011616 DNA binding residues [nucleotide binding] 358220011617 dimerization interface [polypeptide binding]; other site 358220011618 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220011619 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 358220011620 catalytic center binding site [active] 358220011621 ATP binding site [chemical binding]; other site 358220011622 poly(A) polymerase; Region: pcnB; TIGR01942 358220011623 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 358220011624 active site 358220011625 NTP binding site [chemical binding]; other site 358220011626 metal binding triad [ion binding]; metal-binding site 358220011627 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 358220011628 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 358220011629 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 358220011630 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 358220011631 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 358220011632 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220011633 Walker A motif; other site 358220011634 ATP binding site [chemical binding]; other site 358220011635 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 358220011636 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220011637 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220011638 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 358220011639 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 358220011640 dimerization interface [polypeptide binding]; other site 358220011641 putative ATP binding site [chemical binding]; other site 358220011642 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 358220011643 Esterase PHB depolymerase; Region: Esterase_phd; pfam10503 358220011644 Isochorismatase family; Region: Isochorismatase; pfam00857 358220011645 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 358220011646 catalytic triad [active] 358220011647 conserved cis-peptide bond; other site 358220011648 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 358220011649 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 358220011650 conserved cys residue [active] 358220011651 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 358220011652 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 358220011653 conserved cys residue [active] 358220011654 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220011655 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220011656 GAF domain; Region: GAF; pfam01590 358220011657 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 358220011658 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 358220011659 Uncharacterized bacterial subgroup of the Salmonella typhimurium Zn2+ transporter ZntB-like subfamily; Region: ZntB_u1; cd12834 358220011660 Cl binding site [ion binding]; other site 358220011661 oligomer interface [polypeptide binding]; other site 358220011662 Uncharacterized conserved protein [Function unknown]; Region: COG2912 358220011663 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 358220011664 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 358220011665 MviN-like protein; Region: MVIN; pfam03023 358220011666 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 358220011667 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 358220011668 acetylornithine aminotransferase; Provisional; Region: PRK02627 358220011669 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 358220011670 inhibitor-cofactor binding pocket; inhibition site 358220011671 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220011672 catalytic residue [active] 358220011673 ornithine carbamoyltransferase; Provisional; Region: PRK00779 358220011674 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 358220011675 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 358220011676 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4339 358220011677 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 358220011678 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 358220011679 G1 box; other site 358220011680 GTP/Mg2+ binding site [chemical binding]; other site 358220011681 Switch I region; other site 358220011682 G2 box; other site 358220011683 G3 box; other site 358220011684 Switch II region; other site 358220011685 G4 box; other site 358220011686 G5 box; other site 358220011687 Nucleoside recognition; Region: Gate; pfam07670 358220011688 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 358220011689 Nucleoside recognition; Region: Gate; pfam07670 358220011690 FeoA domain; Region: FeoA; pfam04023 358220011691 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 358220011692 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220011693 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 358220011694 putative transposase OrfB; Reviewed; Region: PHA02517 358220011695 Integrase core domain; Region: rve; pfam00665 358220011696 Integrase core domain; Region: rve_3; pfam13683 358220011697 Homeodomain-like domain; Region: HTH_23; cl17451 358220011698 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 358220011699 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 358220011700 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220011701 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011702 active site 358220011703 phosphorylation site [posttranslational modification] 358220011704 intermolecular recognition site; other site 358220011705 dimerization interface [polypeptide binding]; other site 358220011706 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220011707 DNA binding site [nucleotide binding] 358220011708 HAMP domain; Region: HAMP; pfam00672 358220011709 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220011710 dimer interface [polypeptide binding]; other site 358220011711 phosphorylation site [posttranslational modification] 358220011712 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220011713 ATP binding site [chemical binding]; other site 358220011714 Mg2+ binding site [ion binding]; other site 358220011715 G-X-G motif; other site 358220011716 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 358220011717 Putative cyclase; Region: Cyclase; cl00814 358220011718 Kynureninase [Amino acid transport and metabolism]; Region: COG3844 358220011719 kynureninase; Region: kynureninase; TIGR01814 358220011720 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220011721 catalytic residue [active] 358220011722 tryptophan 2,3-dioxygenase; Region: trp_2_3_diox; TIGR03036 358220011723 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 358220011724 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220011725 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220011726 putative substrate translocation pore; other site 358220011727 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 358220011728 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 358220011729 DNA binding residues [nucleotide binding] 358220011730 SpoVR family protein; Provisional; Region: PRK11767 358220011731 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 358220011732 hypothetical protein; Provisional; Region: PRK05325 358220011733 PrkA family serine protein kinase; Provisional; Region: PRK15455 358220011734 AAA ATPase domain; Region: AAA_16; pfam13191 358220011735 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 358220011736 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220011737 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 358220011738 PAS fold; Region: PAS_7; pfam12860 358220011739 PAS domain S-box; Region: sensory_box; TIGR00229 358220011740 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011741 putative active site [active] 358220011742 heme pocket [chemical binding]; other site 358220011743 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220011744 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220011745 metal binding site [ion binding]; metal-binding site 358220011746 active site 358220011747 I-site; other site 358220011748 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220011749 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011750 PAS fold; Region: PAS_3; pfam08447 358220011751 putative active site [active] 358220011752 heme pocket [chemical binding]; other site 358220011753 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011754 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220011755 putative active site [active] 358220011756 heme pocket [chemical binding]; other site 358220011757 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220011758 putative active site [active] 358220011759 heme pocket [chemical binding]; other site 358220011760 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220011761 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220011762 metal binding site [ion binding]; metal-binding site 358220011763 active site 358220011764 I-site; other site 358220011765 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220011766 aconitate hydratase; Validated; Region: PRK09277 358220011767 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 358220011768 substrate binding site [chemical binding]; other site 358220011769 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 358220011770 ligand binding site [chemical binding]; other site 358220011771 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 358220011772 substrate binding site [chemical binding]; other site 358220011773 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 358220011774 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220011775 non-specific DNA binding site [nucleotide binding]; other site 358220011776 salt bridge; other site 358220011777 sequence-specific DNA binding site [nucleotide binding]; other site 358220011778 H-NS histone family; Region: Histone_HNS; pfam00816 358220011779 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 358220011780 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 358220011781 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 358220011782 active site 358220011783 metal binding site [ion binding]; metal-binding site 358220011784 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 358220011785 DEAD-like helicases superfamily; Region: DEXDc; smart00487 358220011786 ATP binding site [chemical binding]; other site 358220011787 Mg++ binding site [ion binding]; other site 358220011788 motif III; other site 358220011789 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220011790 nucleotide binding region [chemical binding]; other site 358220011791 ATP-binding site [chemical binding]; other site 358220011792 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 358220011793 FtsX-like permease family; Region: FtsX; pfam02687 358220011794 Peptidase C13 family; Region: Peptidase_C13; cl02159 358220011795 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 358220011796 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 358220011797 Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]; Region: FdnI; COG2864 358220011798 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 358220011799 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 358220011800 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 358220011801 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 358220011802 [4Fe-4S] binding site [ion binding]; other site 358220011803 molybdopterin cofactor binding site; other site 358220011804 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 358220011805 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 358220011806 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 358220011807 molybdopterin cofactor binding site; other site 358220011808 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 358220011809 4Fe-4S binding domain; Region: Fer4; pfam00037 358220011810 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 358220011811 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 358220011812 4Fe-4S binding domain; Region: Fer4; pfam00037 358220011813 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 358220011814 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 358220011815 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 358220011816 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 358220011817 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220011818 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 358220011819 catalytic loop [active] 358220011820 iron binding site [ion binding]; other site 358220011821 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 358220011822 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 358220011823 [4Fe-4S] binding site [ion binding]; other site 358220011824 molybdopterin cofactor binding site; other site 358220011825 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 358220011826 molybdopterin cofactor binding site; other site 358220011827 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 358220011828 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH...; Region: TRX_Fd_NuoE_W_FDH_beta; cd03082 358220011829 putative dimer interface [polypeptide binding]; other site 358220011830 [2Fe-2S] cluster binding site [ion binding]; other site 358220011831 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 358220011832 SLBB domain; Region: SLBB; pfam10531 358220011833 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 358220011834 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220011835 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220011836 dimerization interface [polypeptide binding]; other site 358220011837 antiporter inner membrane protein; Provisional; Region: PRK11670 358220011838 Domain of unknown function DUF59; Region: DUF59; pfam01883 358220011839 MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions...; Region: MRP-like; cd02037 358220011840 Walker A motif; other site 358220011841 Restriction endonuclease; Region: Mrr_cat; pfam04471 358220011842 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 358220011843 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 358220011844 Strictosidine synthase; Region: Str_synth; pfam03088 358220011845 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 358220011846 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 358220011847 active site 358220011848 HIGH motif; other site 358220011849 KMSKS motif; other site 358220011850 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 358220011851 tRNA binding surface [nucleotide binding]; other site 358220011852 anticodon binding site; other site 358220011853 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 358220011854 dimer interface [polypeptide binding]; other site 358220011855 putative tRNA-binding site [nucleotide binding]; other site 358220011856 Uncharacterized conserved protein [Function unknown]; Region: COG1284 358220011857 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 358220011858 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 358220011859 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 358220011860 L-aspartate oxidase; Provisional; Region: PRK09077 358220011861 L-aspartate oxidase; Provisional; Region: PRK06175 358220011862 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 358220011863 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 358220011864 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220011865 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 358220011866 active site 358220011867 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 358220011868 tetramerization interface [polypeptide binding]; other site 358220011869 active site 358220011870 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 358220011871 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 358220011872 inhibitor-cofactor binding pocket; inhibition site 358220011873 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220011874 catalytic residue [active] 358220011875 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 358220011876 AAA domain; Region: AAA_26; pfam13500 358220011877 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 358220011878 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 358220011879 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 358220011880 catalytic residue [active] 358220011881 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 358220011882 putative substrate binding pocket [chemical binding]; other site 358220011883 trimer interface [polypeptide binding]; other site 358220011884 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220011885 chorismate binding enzyme; Region: Chorismate_bind; cl10555 358220011886 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 358220011887 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 358220011888 substrate-cofactor binding pocket; other site 358220011889 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220011890 quinolinate synthetase; Provisional; Region: PRK09375 358220011891 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 358220011892 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 358220011893 dimerization interface [polypeptide binding]; other site 358220011894 active site 358220011895 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 358220011896 oligomerization interface [polypeptide binding]; other site 358220011897 active site 358220011898 metal binding site [ion binding]; metal-binding site 358220011899 Pantoate-beta-alanine ligase; Region: PanC; cd00560 358220011900 pantoate--beta-alanine ligase; Region: panC; TIGR00018 358220011901 active site 358220011902 ATP-binding site [chemical binding]; other site 358220011903 pantoate-binding site; other site 358220011904 HXXH motif; other site 358220011905 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 358220011906 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 358220011907 catalytic site [active] 358220011908 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 358220011909 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 358220011910 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 358220011911 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 358220011912 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 358220011913 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 358220011914 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 358220011915 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 358220011916 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 358220011917 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 358220011918 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 358220011919 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 358220011920 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 358220011921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 358220011922 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 358220011923 Uncharacterized conserved protein [Function unknown]; Region: COG2308 358220011924 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4307 358220011925 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 358220011926 BON domain; Region: BON; pfam04972 358220011927 CHASE3 domain; Region: CHASE3; pfam05227 358220011928 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220011929 Histidine kinase; Region: HisKA_3; pfam07730 358220011930 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220011931 ATP binding site [chemical binding]; other site 358220011932 Mg2+ binding site [ion binding]; other site 358220011933 G-X-G motif; other site 358220011934 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220011935 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011936 active site 358220011937 phosphorylation site [posttranslational modification] 358220011938 intermolecular recognition site; other site 358220011939 dimerization interface [polypeptide binding]; other site 358220011940 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220011941 DNA binding residues [nucleotide binding] 358220011942 dimerization interface [polypeptide binding]; other site 358220011943 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220011944 Response regulator receiver domain; Region: Response_reg; pfam00072 358220011945 active site 358220011946 phosphorylation site [posttranslational modification] 358220011947 intermolecular recognition site; other site 358220011948 dimerization interface [polypeptide binding]; other site 358220011949 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 358220011950 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 358220011951 ATP binding site [chemical binding]; other site 358220011952 substrate interface [chemical binding]; other site 358220011953 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 358220011954 C-terminal peptidase (prc); Region: prc; TIGR00225 358220011955 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 358220011956 protein binding site [polypeptide binding]; other site 358220011957 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 358220011958 Catalytic dyad [active] 358220011959 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 358220011960 catalytic core [active] 358220011961 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 358220011962 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 358220011963 active site residue [active] 358220011964 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 358220011965 GSH binding site [chemical binding]; other site 358220011966 catalytic residues [active] 358220011967 preprotein translocase subunit SecB; Validated; Region: PRK05751 358220011968 SecA binding site; other site 358220011969 Preprotein binding site; other site 358220011970 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 358220011971 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 358220011972 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 358220011973 diaminopimelate decarboxylase; Provisional; Region: PRK11165 358220011974 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 358220011975 active site 358220011976 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 358220011977 substrate binding site [chemical binding]; other site 358220011978 catalytic residues [active] 358220011979 dimer interface [polypeptide binding]; other site 358220011980 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220011981 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220011982 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220011983 dimerization interface [polypeptide binding]; other site 358220011984 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 358220011985 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 358220011986 active site 358220011987 (T/H)XGH motif; other site 358220011988 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 358220011989 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220011990 S-adenosylmethionine binding site [chemical binding]; other site 358220011991 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 358220011992 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 358220011993 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 358220011994 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 358220011995 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 358220011996 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 358220011997 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 358220011998 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 358220011999 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220012000 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 358220012001 putative active site [active] 358220012002 heme pocket [chemical binding]; other site 358220012003 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220012004 putative active site [active] 358220012005 heme pocket [chemical binding]; other site 358220012006 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220012007 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220012008 metal binding site [ion binding]; metal-binding site 358220012009 active site 358220012010 I-site; other site 358220012011 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220012012 Family description; Region: VCBS; pfam13517 358220012013 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 358220012014 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 358220012015 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220012016 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220012017 DNA binding residues [nucleotide binding] 358220012018 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220012019 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 358220012020 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 358220012021 Cu(I) binding site [ion binding]; other site 358220012022 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 358220012023 UbiA prenyltransferase family; Region: UbiA; pfam01040 358220012024 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 358220012025 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 358220012026 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 358220012027 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 358220012028 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 358220012029 Subunit III/VIIa interface [polypeptide binding]; other site 358220012030 Phospholipid binding site [chemical binding]; other site 358220012031 Subunit I/III interface [polypeptide binding]; other site 358220012032 Subunit III/VIb interface [polypeptide binding]; other site 358220012033 Subunit III/VIa interface; other site 358220012034 Subunit III/Vb interface [polypeptide binding]; other site 358220012035 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 358220012036 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 358220012037 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 358220012038 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 358220012039 Subunit I/III interface [polypeptide binding]; other site 358220012040 D-pathway; other site 358220012041 Subunit I/VIIc interface [polypeptide binding]; other site 358220012042 Subunit I/IV interface [polypeptide binding]; other site 358220012043 Subunit I/II interface [polypeptide binding]; other site 358220012044 Low-spin heme (heme a) binding site [chemical binding]; other site 358220012045 Subunit I/VIIa interface [polypeptide binding]; other site 358220012046 Subunit I/VIa interface [polypeptide binding]; other site 358220012047 Dimer interface; other site 358220012048 Putative water exit pathway; other site 358220012049 Binuclear center (heme a3/CuB) [ion binding]; other site 358220012050 K-pathway; other site 358220012051 Subunit I/Vb interface [polypeptide binding]; other site 358220012052 Putative proton exit pathway; other site 358220012053 Subunit I/VIb interface; other site 358220012054 Subunit I/VIc interface [polypeptide binding]; other site 358220012055 Electron transfer pathway; other site 358220012056 Subunit I/VIIIb interface [polypeptide binding]; other site 358220012057 Subunit I/VIIb interface [polypeptide binding]; other site 358220012058 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 358220012059 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 358220012060 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 358220012061 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 358220012062 Cytochrome c; Region: Cytochrom_C; pfam00034 358220012063 Integral membrane protein (DUF2244); Region: DUF2244; pfam10003 358220012064 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220012065 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 358220012066 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 358220012067 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220012068 active site 358220012069 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 358220012070 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220012071 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220012072 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220012073 putative effector binding pocket; other site 358220012074 dimerization interface [polypeptide binding]; other site 358220012075 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 358220012076 putative active site [active] 358220012077 putative catalytic site [active] 358220012078 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 358220012079 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 358220012080 P-loop; other site 358220012081 Magnesium ion binding site [ion binding]; other site 358220012082 LysE type translocator; Region: LysE; cl00565 358220012083 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 358220012084 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 358220012085 TrkA-N domain; Region: TrkA_N; pfam02254 358220012086 UPF0126 domain; Region: UPF0126; pfam03458 358220012087 Predicted membrane protein [Function unknown]; Region: COG2860 358220012088 UPF0126 domain; Region: UPF0126; pfam03458 358220012089 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 358220012090 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 358220012091 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220012092 CoenzymeA binding site [chemical binding]; other site 358220012093 subunit interaction site [polypeptide binding]; other site 358220012094 PHB binding site; other site 358220012095 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220012096 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220012097 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220012098 dimerization interface [polypeptide binding]; other site 358220012099 Lin1944 and related proteins, classical (c) SDRs; Region: Lin1944_like_SDR_c; cd11731 358220012100 putative NAD(P) binding site [chemical binding]; other site 358220012101 homodimer interface [polypeptide binding]; other site 358220012102 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220012103 classical (c) SDRs; Region: SDR_c; cd05233 358220012104 short chain dehydrogenase; Provisional; Region: PRK07577 358220012105 NAD(P) binding site [chemical binding]; other site 358220012106 active site 358220012107 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 358220012108 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220012109 dimer interface [polypeptide binding]; other site 358220012110 active site 358220012111 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 358220012112 3-oxoacid CoA-transferase, A subunit; Region: pcaI_scoA_fam; TIGR02429 358220012113 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 358220012114 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 358220012115 Bacterial transcriptional regulator; Region: IclR; pfam01614 358220012116 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 358220012117 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 358220012118 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 358220012119 tetramer interface [polypeptide binding]; other site 358220012120 active site 358220012121 Mg2+/Mn2+ binding site [ion binding]; other site 358220012122 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 358220012123 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220012124 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220012125 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220012126 Walker A/P-loop; other site 358220012127 ATP binding site [chemical binding]; other site 358220012128 Q-loop/lid; other site 358220012129 ABC transporter signature motif; other site 358220012130 Walker B; other site 358220012131 D-loop; other site 358220012132 H-loop/switch region; other site 358220012133 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220012134 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220012135 Walker A/P-loop; other site 358220012136 ATP binding site [chemical binding]; other site 358220012137 Q-loop/lid; other site 358220012138 ABC transporter signature motif; other site 358220012139 Walker B; other site 358220012140 D-loop; other site 358220012141 H-loop/switch region; other site 358220012142 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220012143 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220012144 TM-ABC transporter signature motif; other site 358220012145 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220012146 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220012147 TM-ABC transporter signature motif; other site 358220012148 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 358220012149 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 358220012150 substrate binding site [chemical binding]; other site 358220012151 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 358220012152 substrate binding site [chemical binding]; other site 358220012153 ligand binding site [chemical binding]; other site 358220012154 Transcriptional regulator [Transcription]; Region: IclR; COG1414 358220012155 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 358220012156 Bacterial transcriptional regulator; Region: IclR; pfam01614 358220012157 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 358220012158 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 358220012159 Cytochrome c553 [Energy production and conversion]; Region: COG2863 358220012160 Cytochrome c; Region: Cytochrom_C; cl11414 358220012161 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 358220012162 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220012163 Walker A motif; other site 358220012164 ATP binding site [chemical binding]; other site 358220012165 Walker B motif; other site 358220012166 arginine finger; other site 358220012167 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 358220012168 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 358220012169 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 358220012170 Surface antigen; Region: Bac_surface_Ag; pfam01103 358220012171 Family of unknown function (DUF490); Region: DUF490; pfam04357 358220012172 threonine and homoserine efflux system; Provisional; Region: PRK10532 358220012173 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220012174 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 358220012175 putative DNA binding site [nucleotide binding]; other site 358220012176 putative Zn2+ binding site [ion binding]; other site 358220012177 AsnC family; Region: AsnC_trans_reg; pfam01037 358220012178 2-dehydropantoate 2-reductase; Provisional; Region: PRK08229 358220012179 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 358220012180 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 358220012181 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220012182 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 358220012183 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220012184 dimer interface [polypeptide binding]; other site 358220012185 phosphorylation site [posttranslational modification] 358220012186 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220012187 ATP binding site [chemical binding]; other site 358220012188 Mg2+ binding site [ion binding]; other site 358220012189 G-X-G motif; other site 358220012190 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220012191 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220012192 active site 358220012193 phosphorylation site [posttranslational modification] 358220012194 intermolecular recognition site; other site 358220012195 dimerization interface [polypeptide binding]; other site 358220012196 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220012197 DNA binding site [nucleotide binding] 358220012198 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 358220012199 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 358220012200 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 358220012201 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 358220012202 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 358220012203 protein binding site [polypeptide binding]; other site 358220012204 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 358220012205 protein binding site [polypeptide binding]; other site 358220012206 Catalase-like heme-binding proteins and protein domains; Region: catalase_like; cl09506 358220012207 heme binding pocket [chemical binding]; other site 358220012208 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 358220012209 active site 358220012210 catalytic residues [active] 358220012211 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220012212 EamA-like transporter family; Region: EamA; pfam00892 358220012213 EamA-like transporter family; Region: EamA; pfam00892 358220012214 galactarate dehydratase; Region: galactar-dH20; TIGR03248 358220012215 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 358220012216 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 358220012217 DctM-like transporters; Region: DctM; pfam06808 358220012218 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 358220012219 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 358220012220 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220012221 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 358220012222 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 358220012223 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 358220012224 extended (e) SDRs; Region: SDR_e; cd08946 358220012225 NAD(P) binding site [chemical binding]; other site 358220012226 active site 358220012227 substrate binding site [chemical binding]; other site 358220012228 Transcriptional regulators [Transcription]; Region: FadR; COG2186 358220012229 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220012230 DNA-binding site [nucleotide binding]; DNA binding site 358220012231 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 358220012232 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 358220012233 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 358220012234 NAD(P) binding site [chemical binding]; other site 358220012235 catalytic residues [active] 358220012236 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 358220012237 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 358220012238 N-terminal plug; other site 358220012239 ligand-binding site [chemical binding]; other site 358220012240 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 358220012241 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 358220012242 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220012243 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220012244 dimer interface [polypeptide binding]; other site 358220012245 phosphorylation site [posttranslational modification] 358220012246 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220012247 ATP binding site [chemical binding]; other site 358220012248 Mg2+ binding site [ion binding]; other site 358220012249 G-X-G motif; other site 358220012250 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 358220012251 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220012252 dimer interface [polypeptide binding]; other site 358220012253 conserved gate region; other site 358220012254 putative PBP binding loops; other site 358220012255 ABC-ATPase subunit interface; other site 358220012256 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 358220012257 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 358220012258 Walker A/P-loop; other site 358220012259 ATP binding site [chemical binding]; other site 358220012260 Q-loop/lid; other site 358220012261 ABC transporter signature motif; other site 358220012262 Walker B; other site 358220012263 D-loop; other site 358220012264 H-loop/switch region; other site 358220012265 TOBE domain; Region: TOBE_2; pfam08402 358220012266 Calx-beta domain; Region: Calx-beta; pfam03160 358220012267 Calx-beta domain; Region: Calx-beta; pfam03160 358220012268 Calx-beta domain; Region: Calx-beta; pfam03160 358220012269 Calx-beta domain; Region: Calx-beta; cl02522 358220012270 Calx-beta domain; Region: Calx-beta; pfam03160 358220012271 Calx-beta domain; Region: Calx-beta; cl02522 358220012272 Calx-beta domain; Region: Calx-beta; cl02522 358220012273 Domain of unknown function (DUF4214); Region: DUF4214; pfam13946 358220012274 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 358220012275 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 358220012276 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220012277 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220012278 ligand binding site [chemical binding]; other site 358220012279 flexible hinge region; other site 358220012280 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 358220012281 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 358220012282 putative acyl-acceptor binding pocket; other site 358220012283 dihydroorotase; Provisional; Region: PRK07627 358220012284 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 358220012285 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 358220012286 active site 358220012287 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 358220012288 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 358220012289 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 358220012290 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220012291 active site 358220012292 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 358220012293 hypothetical protein; Validated; Region: PRK00228 358220012294 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 358220012295 DNA photolyase; Region: DNA_photolyase; pfam00875 358220012296 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 358220012297 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 358220012298 Walker A motif; other site 358220012299 ATP binding site [chemical binding]; other site 358220012300 Walker B motif; other site 358220012301 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 358220012302 putative binding surface; other site 358220012303 active site 358220012304 Hpt domain; Region: Hpt; pfam01627 358220012305 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 358220012306 putative binding surface; other site 358220012307 active site 358220012308 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 358220012309 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 358220012310 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220012311 ATP binding site [chemical binding]; other site 358220012312 Mg2+ binding site [ion binding]; other site 358220012313 G-X-G motif; other site 358220012314 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 358220012315 Response regulator receiver domain; Region: Response_reg; pfam00072 358220012316 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220012317 active site 358220012318 phosphorylation site [posttranslational modification] 358220012319 intermolecular recognition site; other site 358220012320 dimerization interface [polypeptide binding]; other site 358220012321 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 358220012322 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 358220012323 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220012324 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220012325 dimer interface [polypeptide binding]; other site 358220012326 putative CheW interface [polypeptide binding]; other site 358220012327 Response regulator receiver domain; Region: Response_reg; pfam00072 358220012328 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220012329 active site 358220012330 phosphorylation site [posttranslational modification] 358220012331 intermolecular recognition site; other site 358220012332 dimerization interface [polypeptide binding]; other site 358220012333 Response regulator receiver domain; Region: Response_reg; pfam00072 358220012334 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220012335 active site 358220012336 phosphorylation site [posttranslational modification] 358220012337 intermolecular recognition site; other site 358220012338 dimerization interface [polypeptide binding]; other site 358220012339 Rubredoxin [Energy production and conversion]; Region: COG1773 358220012340 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 358220012341 iron binding site [ion binding]; other site 358220012342 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 358220012343 substrate binding site [chemical binding]; other site 358220012344 ATP binding site [chemical binding]; other site 358220012345 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 358220012346 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 358220012347 inhibitor-cofactor binding pocket; inhibition site 358220012348 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220012349 catalytic residue [active] 358220012350 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 358220012351 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 358220012352 Bacterial transcriptional regulator; Region: IclR; pfam01614 358220012353 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 358220012354 Cytochrome c; Region: Cytochrom_C; cl11414 358220012355 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 358220012356 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 358220012357 purine monophosphate binding site [chemical binding]; other site 358220012358 dimer interface [polypeptide binding]; other site 358220012359 putative catalytic residues [active] 358220012360 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 358220012361 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 358220012362 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 358220012363 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 358220012364 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 358220012365 FMN binding site [chemical binding]; other site 358220012366 active site 358220012367 catalytic residues [active] 358220012368 substrate binding site [chemical binding]; other site 358220012369 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 358220012370 Predicted membrane protein [Function unknown]; Region: COG1238 358220012371 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220012372 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220012373 metal binding site [ion binding]; metal-binding site 358220012374 active site 358220012375 I-site; other site 358220012376 Predicted permeases [General function prediction only]; Region: RarD; COG2962 358220012377 GTP-binding protein YchF; Reviewed; Region: PRK09601 358220012378 YchF GTPase; Region: YchF; cd01900 358220012379 G1 box; other site 358220012380 GTP/Mg2+ binding site [chemical binding]; other site 358220012381 Switch I region; other site 358220012382 G2 box; other site 358220012383 Switch II region; other site 358220012384 G3 box; other site 358220012385 G4 box; other site 358220012386 G5 box; other site 358220012387 TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the...; Region: TGS_YchF_C; cd04867 358220012388 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 358220012389 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 358220012390 MOSC domain; Region: MOSC; pfam03473 358220012391 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220012392 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 358220012393 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 358220012394 dimerization domain [polypeptide binding]; other site 358220012395 dimer interface [polypeptide binding]; other site 358220012396 catalytic residues [active] 358220012397 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 358220012398 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 358220012399 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 358220012400 protein binding site [polypeptide binding]; other site 358220012401 enoyl-CoA hydratase; Provisional; Region: PRK05862 358220012402 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220012403 substrate binding site [chemical binding]; other site 358220012404 oxyanion hole (OAH) forming residues; other site 358220012405 trimer interface [polypeptide binding]; other site 358220012406 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 358220012407 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 358220012408 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220012409 FeS/SAM binding site; other site 358220012410 TRAM domain; Region: TRAM; pfam01938 358220012411 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220012412 dimer interface [polypeptide binding]; other site 358220012413 phosphorylation site [posttranslational modification] 358220012414 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220012415 ATP binding site [chemical binding]; other site 358220012416 Mg2+ binding site [ion binding]; other site 358220012417 G-X-G motif; other site 358220012418 response regulator GlrR; Provisional; Region: PRK15115 358220012419 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220012420 active site 358220012421 phosphorylation site [posttranslational modification] 358220012422 intermolecular recognition site; other site 358220012423 dimerization interface [polypeptide binding]; other site 358220012424 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220012425 Walker A motif; other site 358220012426 ATP binding site [chemical binding]; other site 358220012427 Walker B motif; other site 358220012428 arginine finger; other site 358220012429 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 358220012430 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 358220012431 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 358220012432 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 358220012433 Ligand binding site; other site 358220012434 DXD motif; other site 358220012435 signal recognition particle protein; Provisional; Region: PRK10867 358220012436 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 358220012437 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 358220012438 GTP binding site [chemical binding]; other site 358220012439 Signal peptide binding domain; Region: SRP_SPB; pfam02978 358220012440 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 358220012441 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 358220012442 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220012443 dimer interface [polypeptide binding]; other site 358220012444 phosphorylation site [posttranslational modification] 358220012445 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220012446 ATP binding site [chemical binding]; other site 358220012447 Mg2+ binding site [ion binding]; other site 358220012448 G-X-G motif; other site 358220012449 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 358220012450 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220012451 active site 358220012452 phosphorylation site [posttranslational modification] 358220012453 intermolecular recognition site; other site 358220012454 dimerization interface [polypeptide binding]; other site 358220012455 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220012456 Walker A motif; other site 358220012457 ATP binding site [chemical binding]; other site 358220012458 Walker B motif; other site 358220012459 arginine finger; other site 358220012460 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 358220012461 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 358220012462 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 358220012463 amidase catalytic site [active] 358220012464 Zn binding residues [ion binding]; other site 358220012465 substrate binding site [chemical binding]; other site 358220012466 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 358220012467 ATP cone domain; Region: ATP-cone; pfam03477 358220012468 Class I ribonucleotide reductase; Region: RNR_I; cd01679 358220012469 active site 358220012470 dimer interface [polypeptide binding]; other site 358220012471 catalytic residues [active] 358220012472 effector binding site; other site 358220012473 R2 peptide binding site; other site 358220012474 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 358220012475 dimer interface [polypeptide binding]; other site 358220012476 putative radical transfer pathway; other site 358220012477 diiron center [ion binding]; other site 358220012478 tyrosyl radical; other site 358220012479 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 358220012480 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 358220012481 substrate binding site [chemical binding]; other site 358220012482 ATP binding site [chemical binding]; other site 358220012483 zinc-ribbon domain; Region: zinc_ribbon_5; pfam13719 358220012484 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 358220012485 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 358220012486 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 358220012487 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 358220012488 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 358220012489 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 358220012490 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 358220012491 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 358220012492 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 358220012493 carboxyltransferase (CT) interaction site; other site 358220012494 biotinylation site [posttranslational modification]; other site 358220012495 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 358220012496 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 358220012497 catalytic residues [active] 358220012498 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 358220012499 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 358220012500 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 358220012501 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 358220012502 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 358220012503 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 358220012504 protease TldD; Provisional; Region: tldD; PRK10735 358220012505 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 358220012506 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 358220012507 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 358220012508 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 358220012509 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 358220012510 active site 358220012511 ATP binding site [chemical binding]; other site 358220012512 substrate binding site [chemical binding]; other site 358220012513 activation loop (A-loop); other site 358220012514 HDOD domain; Region: HDOD; pfam08668 358220012515 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 358220012516 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220012517 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 358220012518 O-Antigen ligase; Region: Wzy_C; pfam04932 358220012519 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 358220012520 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 358220012521 RNB domain; Region: RNB; pfam00773 358220012522 TonB C terminal; Region: TonB_2; pfam13103 358220012523 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 358220012524 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 358220012525 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 358220012526 shikimate binding site; other site 358220012527 NAD(P) binding site [chemical binding]; other site 358220012528 Transglycosylase; Region: Transgly; cl17702 358220012529 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 358220012530 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 358220012531 Cytochrome P450; Region: p450; cl12078 358220012532 Helix-turn-helix domain; Region: HTH_18; pfam12833 358220012533 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220012534 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 358220012535 putative acyl-acceptor binding pocket; other site 358220012536 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 358220012537 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 358220012538 Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase [General function prediction only]; Region: COG4589 358220012539 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 358220012540 active site 358220012541 putative DNA-binding cleft [nucleotide binding]; other site 358220012542 dimer interface [polypeptide binding]; other site 358220012543 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 358220012544 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 358220012545 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 358220012546 short chain dehydrogenase; Provisional; Region: PRK06172 358220012547 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220012548 NAD(P) binding site [chemical binding]; other site 358220012549 active site 358220012550 type II secretion system protein F; Region: GspF; TIGR02120 358220012551 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 358220012552 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 358220012553 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 358220012554 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 358220012555 EF-hand domain pair; Region: EF_hand_5; pfam13499 358220012556 Ca2+ binding site [ion binding]; other site 358220012557 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 358220012558 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 358220012559 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 358220012560 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 358220012561 Walker A/P-loop; other site 358220012562 ATP binding site [chemical binding]; other site 358220012563 Q-loop/lid; other site 358220012564 ABC transporter signature motif; other site 358220012565 Walker B; other site 358220012566 D-loop; other site 358220012567 H-loop/switch region; other site 358220012568 cyanophycin synthetase; Provisional; Region: PRK14016 358220012569 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 358220012570 cyanophycin synthetase; Provisional; Region: PRK14016 358220012571 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 358220012572 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 358220012573 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 358220012574 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 358220012575 CreA protein; Region: CreA; pfam05981 358220012576 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 358220012577 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 358220012578 catalytic residues [active] 358220012579 short chain dehydrogenase; Provisional; Region: PRK06125 358220012580 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220012581 NAD(P) binding site [chemical binding]; other site 358220012582 active site 358220012583 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220012584 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 358220012585 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 358220012586 tetramer interface [polypeptide binding]; other site 358220012587 active site 358220012588 Mg2+/Mn2+ binding site [ion binding]; other site 358220012589 Propionate catabolism activator; Region: PrpR_N; pfam06506 358220012590 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 358220012591 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 358220012592 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220012593 Walker A motif; other site 358220012594 ATP binding site [chemical binding]; other site 358220012595 Walker B motif; other site 358220012596 arginine finger; other site 358220012597 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 358220012598 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07656 358220012599 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220012600 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 358220012601 acyl-activating enzyme (AAE) consensus motif; other site 358220012602 acyl-activating enzyme (AAE) consensus motif; other site 358220012603 putative AMP binding site [chemical binding]; other site 358220012604 putative active site [active] 358220012605 putative CoA binding site [chemical binding]; other site 358220012606 acetyl-CoA acetyltransferase; Provisional; Region: PRK07516 358220012607 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 358220012608 active site 358220012609 tellurite resistance protein terB; Region: terB; cd07176 358220012610 putative metal binding site [ion binding]; other site 358220012611 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 358220012612 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 358220012613 Sporulation related domain; Region: SPOR; pfam05036 358220012614 SGNH_hydrolase subfamily, FeeA, FeeB and similar esterases/lipases. FeeA and FeeB are part of a biosynthetic gene cluster and may participate in the biosynthesis of long-chain N-acyltyrosines by providing saturated and unsaturated fatty acids, which it...; Region: FeeA_FeeB_like; cd01836 358220012615 active site 358220012616 catalytic triad [active] 358220012617 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220012618 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_7; cd03862 358220012619 putative active site [active] 358220012620 Zn binding site [ion binding]; other site 358220012621 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 358220012622 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 358220012623 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 358220012624 IHF dimer interface [polypeptide binding]; other site 358220012625 IHF - DNA interface [nucleotide binding]; other site 358220012626 feruloyl-CoA synthase; Reviewed; Region: PRK08180 358220012627 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 358220012628 acyl-activating enzyme (AAE) consensus motif; other site 358220012629 putative active site [active] 358220012630 putative AMP binding site [chemical binding]; other site 358220012631 putative CoA binding site [chemical binding]; other site 358220012632 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220012633 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220012634 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220012635 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220012636 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220012637 ligand binding site [chemical binding]; other site 358220012638 flexible hinge region; other site 358220012639 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 358220012640 non-specific DNA interactions [nucleotide binding]; other site 358220012641 DNA binding site [nucleotide binding] 358220012642 sequence specific DNA binding site [nucleotide binding]; other site 358220012643 putative cAMP binding site [chemical binding]; other site 358220012644 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220012645 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 358220012646 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220012647 acyl-activating enzyme (AAE) consensus motif; other site 358220012648 AMP binding site [chemical binding]; other site 358220012649 active site 358220012650 CoA binding site [chemical binding]; other site 358220012651 aldehyde dehydrogenase; Provisional; Region: PRK11903 358220012652 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 358220012653 NAD(P) binding site [chemical binding]; other site 358220012654 catalytic residues [active] 358220012655 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 358220012656 anaerobic benzoate catabolism transcriptional regulator; Reviewed; Region: PRK08154 358220012657 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 358220012658 non-specific DNA binding site [nucleotide binding]; other site 358220012659 salt bridge; other site 358220012660 sequence-specific DNA binding site [nucleotide binding]; other site 358220012661 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 358220012662 ADP binding site [chemical binding]; other site 358220012663 magnesium binding site [ion binding]; other site 358220012664 putative shikimate binding site; other site 358220012665 benzoyl-CoA-dihydrodiol lyase; Provisional; Region: PRK08184 358220012666 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220012667 substrate binding site [chemical binding]; other site 358220012668 oxyanion hole (OAH) forming residues; other site 358220012669 trimer interface [polypeptide binding]; other site 358220012670 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220012671 trimer interface [polypeptide binding]; other site 358220012672 oxyanion hole (OAH) forming residues; other site 358220012673 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 358220012674 benzoyl-CoA oxygenase/reductase, BoxA protein; Region: benzo_boxA; TIGR03224 358220012675 4Fe-4S binding domain; Region: Fer4; pfam00037 358220012676 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 358220012677 FAD binding pocket [chemical binding]; other site 358220012678 conserved FAD binding motif [chemical binding]; other site 358220012679 phosphate binding motif [ion binding]; other site 358220012680 beta-alpha-beta structure motif; other site 358220012681 NAD binding pocket [chemical binding]; other site 358220012682 Protein of unknown function (DUF3348); Region: DUF3348; pfam11828 358220012683 Domain of unknown function (DUF802); Region: DUF802; pfam05650 358220012684 hypothetical protein; Provisional; Region: PRK09040 358220012685 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 358220012686 ligand binding site [chemical binding]; other site 358220012687 Protein of unknown function (DUF2894); Region: DUF2894; pfam11445 358220012688 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 358220012689 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220012690 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220012691 dimerization interface [polypeptide binding]; other site 358220012692 NADH dehydrogenase subunit L; Provisional; Region: PRK08168 358220012693 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 358220012694 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3002 358220012695 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 358220012696 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220012697 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220012698 metal binding site [ion binding]; metal-binding site 358220012699 active site 358220012700 I-site; other site 358220012701 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220012702 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 358220012703 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 358220012704 glutaminase active site [active] 358220012705 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 358220012706 dimer interface [polypeptide binding]; other site 358220012707 active site 358220012708 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 358220012709 dimer interface [polypeptide binding]; other site 358220012710 active site 358220012711 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220012712 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 358220012713 putative DNA binding site [nucleotide binding]; other site 358220012714 AsnC family; Region: AsnC_trans_reg; pfam01037 358220012715 MASE2 domain; Region: MASE2; pfam05230 358220012716 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220012717 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220012718 metal binding site [ion binding]; metal-binding site 358220012719 active site 358220012720 I-site; other site 358220012721 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220012722 dimer interface [polypeptide binding]; other site 358220012723 phosphorylation site [posttranslational modification] 358220012724 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220012725 ATP binding site [chemical binding]; other site 358220012726 Mg2+ binding site [ion binding]; other site 358220012727 G-X-G motif; other site 358220012728 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 358220012729 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 358220012730 Substrate binding site; other site 358220012731 Mg++ binding site; other site 358220012732 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 358220012733 active site 358220012734 substrate binding site [chemical binding]; other site 358220012735 CoA binding site [chemical binding]; other site 358220012736 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220012737 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220012738 ligand binding site [chemical binding]; other site 358220012739 flexible hinge region; other site 358220012740 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 358220012741 putative switch regulator; other site 358220012742 non-specific DNA interactions [nucleotide binding]; other site 358220012743 DNA binding site [nucleotide binding] 358220012744 sequence specific DNA binding site [nucleotide binding]; other site 358220012745 putative cAMP binding site [chemical binding]; other site 358220012746 Sensors of blue-light using FAD; Region: BLUF; smart01034 358220012747 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 358220012748 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 358220012749 dimer interface [polypeptide binding]; other site 358220012750 active site 358220012751 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220012752 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 358220012753 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 358220012754 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220012755 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220012756 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 358220012757 dimerization interface [polypeptide binding]; other site 358220012758 substrate binding pocket [chemical binding]; other site 358220012759 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 358220012760 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 358220012761 active site 358220012762 HIGH motif; other site 358220012763 dimer interface [polypeptide binding]; other site 358220012764 KMSKS motif; other site 358220012765 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 358220012766 Peptidase family M23; Region: Peptidase_M23; pfam01551 358220012767 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 358220012768 putative transporter; Provisional; Region: PRK10504 358220012769 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220012770 putative substrate translocation pore; other site 358220012771 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 358220012772 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 358220012773 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 358220012774 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 358220012775 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 358220012776 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the...; Region: Ribosomal_L13; cd00392 358220012777 23S rRNA interface [nucleotide binding]; other site 358220012778 L3 interface [polypeptide binding]; other site 358220012779 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 358220012780 Catalytic domain of Protein Kinases; Region: PKc; cd00180 358220012781 active site 358220012782 ATP binding site [chemical binding]; other site 358220012783 substrate binding site [chemical binding]; other site 358220012784 activation loop (A-loop); other site 358220012785 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 358220012786 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 358220012787 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 358220012788 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 358220012789 FAD binding site [chemical binding]; other site 358220012790 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 358220012791 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 358220012792 FtsJ-like methyltransferase; Region: FtsJ; cl17430 358220012793 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 358220012794 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 358220012795 homotetramer interface [polypeptide binding]; other site 358220012796 ligand binding site [chemical binding]; other site 358220012797 catalytic site [active] 358220012798 NAD binding site [chemical binding]; other site 358220012799 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 358220012800 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 358220012801 G1 box; other site 358220012802 putative GEF interaction site [polypeptide binding]; other site 358220012803 GTP/Mg2+ binding site [chemical binding]; other site 358220012804 Switch I region; other site 358220012805 G2 box; other site 358220012806 G3 box; other site 358220012807 Switch II region; other site 358220012808 G4 box; other site 358220012809 G5 box; other site 358220012810 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 358220012811 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 358220012812 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220012813 active site 358220012814 motif I; other site 358220012815 motif II; other site 358220012816 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220012817 Integrase core domain; Region: rve; pfam00665 358220012818 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220012819 Helix-turn-helix domain; Region: HTH_38; pfam13936 358220012820 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 358220012821 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 358220012822 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 358220012823 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220012824 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220012825 Walker A/P-loop; other site 358220012826 ATP binding site [chemical binding]; other site 358220012827 Q-loop/lid; other site 358220012828 ABC transporter signature motif; other site 358220012829 Walker B; other site 358220012830 D-loop; other site 358220012831 H-loop/switch region; other site 358220012832 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220012833 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 358220012834 TM-ABC transporter signature motif; other site 358220012835 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 358220012836 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 358220012837 ligand binding site [chemical binding]; other site 358220012838 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 358220012839 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 358220012840 substrate binding site [chemical binding]; other site 358220012841 ATP binding site [chemical binding]; other site 358220012842 LabA_like proteins; Region: LabA_like; cd06167 358220012843 putative metal binding site [ion binding]; other site 358220012844 Uncharacterized conserved protein [Function unknown]; Region: COG1432 358220012845 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 358220012846 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220012847 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220012848 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220012849 putative DNA binding site [nucleotide binding]; other site 358220012850 putative Zn2+ binding site [ion binding]; other site 358220012851 AsnC family; Region: AsnC_trans_reg; pfam01037 358220012852 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 358220012853 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 358220012854 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 358220012855 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220012856 Walker A/P-loop; other site 358220012857 ATP binding site [chemical binding]; other site 358220012858 Q-loop/lid; other site 358220012859 ABC transporter signature motif; other site 358220012860 Walker B; other site 358220012861 D-loop; other site 358220012862 H-loop/switch region; other site 358220012863 excinuclease ABC, A subunit; Region: uvra; TIGR00630 358220012864 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220012865 Walker A/P-loop; other site 358220012866 ATP binding site [chemical binding]; other site 358220012867 Q-loop/lid; other site 358220012868 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 358220012869 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 358220012870 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220012871 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220012872 putative ligand binding site [chemical binding]; other site 358220012873 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220012874 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 358220012875 putative ligand binding site [chemical binding]; other site 358220012876 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220012877 putative substrate translocation pore; other site 358220012878 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 358220012879 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 358220012880 putative catalytic residue [active] 358220012881 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 358220012882 This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro)...; Region: ProX_deacylase; cd04333 358220012883 putative deacylase active site [active] 358220012884 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 358220012885 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 358220012886 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220012887 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 358220012888 Protein export membrane protein; Region: SecD_SecF; cl14618 358220012889 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 358220012890 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 358220012891 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 358220012892 active site 358220012893 catalytic residues [active] 358220012894 metal binding site [ion binding]; metal-binding site 358220012895 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220012896 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220012897 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 358220012898 putative dimerization interface [polypeptide binding]; other site 358220012899 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK06130 358220012900 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220012901 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 358220012902 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 358220012903 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220012904 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; Region: GDH_like_2; cd12164 358220012905 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 358220012906 putative ligand binding site [chemical binding]; other site 358220012907 NAD binding site [chemical binding]; other site 358220012908 dimerization interface [polypeptide binding]; other site 358220012909 catalytic site [active] 358220012910 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 358220012911 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 358220012912 ATP-grasp domain; Region: ATP-grasp_4; cl17255 358220012913 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 358220012914 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 358220012915 carboxyltransferase (CT) interaction site; other site 358220012916 biotinylation site [posttranslational modification]; other site 358220012917 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 358220012918 enoyl-CoA hydratase; Provisional; Region: PRK05995 358220012919 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220012920 substrate binding site [chemical binding]; other site 358220012921 oxyanion hole (OAH) forming residues; other site 358220012922 trimer interface [polypeptide binding]; other site 358220012923 DinB family; Region: DinB; cl17821 358220012924 DinB superfamily; Region: DinB_2; pfam12867 358220012925 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 358220012926 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 358220012927 AMP-binding domain protein; Validated; Region: PRK08315 358220012928 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220012929 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 358220012930 acyl-activating enzyme (AAE) consensus motif; other site 358220012931 putative AMP binding site [chemical binding]; other site 358220012932 putative active site [active] 358220012933 putative CoA binding site [chemical binding]; other site 358220012934 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 358220012935 Helix-turn-helix domain; Region: HTH_18; pfam12833 358220012936 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220012937 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 358220012938 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220012939 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220012940 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220012941 dimerization interface [polypeptide binding]; other site 358220012942 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 358220012943 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 358220012944 NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; Region: Octopine_DH; pfam02317 358220012945 potential frameshift: common BLAST hit: gi|222112501|ref|YP_002554765.1| transposase mutator type 358220012946 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 358220012947 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220012948 putative C-terminal domain interface [polypeptide binding]; other site 358220012949 putative GSH binding site (G-site) [chemical binding]; other site 358220012950 putative dimer interface [polypeptide binding]; other site 358220012951 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 358220012952 N-terminal domain interface [polypeptide binding]; other site 358220012953 dimer interface [polypeptide binding]; other site 358220012954 substrate binding pocket (H-site) [chemical binding]; other site 358220012955 6-phosphogluconate phosphatase; Provisional; Region: PRK10563 358220012956 hypothetical protein; Provisional; Region: PRK01842 358220012957 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 358220012958 Predicted membrane protein [Function unknown]; Region: COG2323 358220012959 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; pfam09996 358220012960 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 358220012961 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220012962 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220012963 active site 358220012964 phosphorylation site [posttranslational modification] 358220012965 intermolecular recognition site; other site 358220012966 dimerization interface [polypeptide binding]; other site 358220012967 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220012968 DNA binding residues [nucleotide binding] 358220012969 dimerization interface [polypeptide binding]; other site 358220012970 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 358220012971 TPR motif; other site 358220012972 binding surface 358220012973 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220012974 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220012975 dimer interface [polypeptide binding]; other site 358220012976 phosphorylation site [posttranslational modification] 358220012977 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220012978 Mg2+ binding site [ion binding]; other site 358220012979 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220012980 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220012981 active site 358220012982 C factor cell-cell signaling protein; Provisional; Region: PRK09009 358220012983 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 358220012984 NADP binding site [chemical binding]; other site 358220012985 homodimer interface [polypeptide binding]; other site 358220012986 active site 358220012987 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 358220012988 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220012989 dimer interface [polypeptide binding]; other site 358220012990 active site 358220012991 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 358220012992 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 358220012993 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 358220012994 active site clefts [active] 358220012995 zinc binding site [ion binding]; other site 358220012996 dimer interface [polypeptide binding]; other site 358220012997 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 358220012998 isovaleryl-CoA dehydrogenase; Region: PLN02519 358220012999 substrate binding site [chemical binding]; other site 358220013000 FAD binding site [chemical binding]; other site 358220013001 catalytic base [active] 358220013002 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 358220013003 CoenzymeA binding site [chemical binding]; other site 358220013004 subunit interaction site [polypeptide binding]; other site 358220013005 PHB binding site; other site 358220013006 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 358220013007 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 358220013008 DNA binding residues [nucleotide binding] 358220013009 putative dimer interface [polypeptide binding]; other site 358220013010 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 358220013011 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 358220013012 RibD C-terminal domain; Region: RibD_C; cl17279 358220013013 ABC transporter ATPase component; Reviewed; Region: PRK11147 358220013014 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 358220013015 Walker A/P-loop; other site 358220013016 ATP binding site [chemical binding]; other site 358220013017 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 358220013018 ABC transporter signature motif; other site 358220013019 Walker B; other site 358220013020 ABC transporter; Region: ABC_tran_2; pfam12848 358220013021 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 358220013022 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 358220013023 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013024 active site 358220013025 phosphorylation site [posttranslational modification] 358220013026 intermolecular recognition site; other site 358220013027 dimerization interface [polypeptide binding]; other site 358220013028 CheB methylesterase; Region: CheB_methylest; pfam01339 358220013029 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 358220013030 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 358220013031 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 358220013032 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220013033 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 358220013034 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 358220013035 putative binding surface; other site 358220013036 active site 358220013037 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 358220013038 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220013039 ATP binding site [chemical binding]; other site 358220013040 Mg2+ binding site [ion binding]; other site 358220013041 G-X-G motif; other site 358220013042 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 358220013043 Response regulator receiver domain; Region: Response_reg; pfam00072 358220013044 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013045 active site 358220013046 phosphorylation site [posttranslational modification] 358220013047 intermolecular recognition site; other site 358220013048 dimerization interface [polypeptide binding]; other site 358220013049 Response regulator receiver domain; Region: Response_reg; pfam00072 358220013050 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013051 active site 358220013052 phosphorylation site [posttranslational modification] 358220013053 intermolecular recognition site; other site 358220013054 dimerization interface [polypeptide binding]; other site 358220013055 Histidine kinase; Region: HisKA_3; pfam07730 358220013056 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 358220013057 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220013058 ATP binding site [chemical binding]; other site 358220013059 Mg2+ binding site [ion binding]; other site 358220013060 G-X-G motif; other site 358220013061 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220013062 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013063 active site 358220013064 phosphorylation site [posttranslational modification] 358220013065 intermolecular recognition site; other site 358220013066 dimerization interface [polypeptide binding]; other site 358220013067 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220013068 DNA binding residues [nucleotide binding] 358220013069 dimerization interface [polypeptide binding]; other site 358220013070 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 358220013071 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 358220013072 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 358220013073 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 358220013074 flagellar motor switch protein; Validated; Region: fliN; PRK05698 358220013075 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 358220013076 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 358220013077 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 358220013078 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 358220013079 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 358220013080 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 358220013081 Flagellar FliJ protein; Region: FliJ; pfam02050 358220013082 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 358220013083 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 358220013084 Walker A motif/ATP binding site; other site 358220013085 Walker B motif; other site 358220013086 Flagellar assembly protein FliH; Region: FliH; pfam02108 358220013087 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 358220013088 FliG C-terminal domain; Region: FliG_C; pfam01706 358220013089 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 358220013090 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 358220013091 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 358220013092 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 358220013093 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220013094 Integrase core domain; Region: rve; pfam00665 358220013095 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 358220013096 Helix-turn-helix domain; Region: HTH_38; pfam13936 358220013097 Flagellar protein FliT; Region: FliT; pfam05400 358220013098 flagellar protein FliS; Validated; Region: fliS; PRK05685 358220013099 flagellar capping protein; Reviewed; Region: fliD; PRK08032 358220013100 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 358220013101 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 358220013102 flagellin; Provisional; Region: PRK12806 358220013103 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 358220013104 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 358220013105 flagellin; Provisional; Region: PRK12806 358220013106 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 358220013107 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 358220013108 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 358220013109 flagellar motor protein MotA; Validated; Region: PRK09110 358220013110 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 358220013111 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 358220013112 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 358220013113 ligand binding site [chemical binding]; other site 358220013114 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 358220013115 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013116 active site 358220013117 phosphorylation site [posttranslational modification] 358220013118 intermolecular recognition site; other site 358220013119 dimerization interface [polypeptide binding]; other site 358220013120 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 358220013121 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 358220013122 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 358220013123 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 358220013124 FHIPEP family; Region: FHIPEP; pfam00771 358220013125 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 358220013126 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 358220013127 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 358220013128 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220013129 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 358220013130 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220013131 DNA binding residues [nucleotide binding] 358220013132 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 358220013133 SAF-like; Region: SAF_2; pfam13144 358220013134 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 358220013135 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 358220013136 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 358220013137 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 358220013138 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 358220013139 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 358220013140 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 358220013141 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 358220013142 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 358220013143 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 358220013144 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 358220013145 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 358220013146 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 358220013147 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 358220013148 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 358220013149 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 358220013150 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 358220013151 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 358220013152 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 358220013153 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 358220013154 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 358220013155 Flagellar L-ring protein; Region: FlgH; pfam02107 358220013156 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 358220013157 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 358220013158 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 358220013159 Rod binding protein; Region: Rod-binding; cl01626 358220013160 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 358220013161 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 358220013162 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 358220013163 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 358220013164 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 358220013165 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 358220013166 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 358220013167 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 358220013168 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220013169 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 358220013170 DNA-binding site [nucleotide binding]; DNA binding site 358220013171 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220013172 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220013173 homodimer interface [polypeptide binding]; other site 358220013174 catalytic residue [active] 358220013175 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 358220013176 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 358220013177 EamA-like transporter family; Region: EamA; pfam00892 358220013178 Cupin domain; Region: Cupin_2; cl17218 358220013179 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 358220013180 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 358220013181 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220013182 homodimer interface [polypeptide binding]; other site 358220013183 catalytic residue [active] 358220013184 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220013185 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_2; cd03047 358220013186 putative C-terminal domain interface [polypeptide binding]; other site 358220013187 putative GSH binding site (G-site) [chemical binding]; other site 358220013188 putative dimer interface [polypeptide binding]; other site 358220013189 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 358220013190 putative N-terminal domain interface [polypeptide binding]; other site 358220013191 putative dimer interface [polypeptide binding]; other site 358220013192 putative substrate binding pocket (H-site) [chemical binding]; other site 358220013193 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 358220013194 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 358220013195 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 358220013196 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 358220013197 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 358220013198 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 358220013199 tetramer interface [polypeptide binding]; other site 358220013200 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220013201 catalytic residue [active] 358220013202 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 358220013203 catalytic core [active] 358220013204 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 358220013205 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 358220013206 PGAP1-like protein; Region: PGAP1; pfam07819 358220013207 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 358220013208 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220013209 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 358220013210 acyl-activating enzyme (AAE) consensus motif; other site 358220013211 putative AMP binding site [chemical binding]; other site 358220013212 putative active site [active] 358220013213 putative CoA binding site [chemical binding]; other site 358220013214 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 358220013215 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 358220013216 ligand binding site [chemical binding]; other site 358220013217 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 358220013218 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 358220013219 Walker A/P-loop; other site 358220013220 ATP binding site [chemical binding]; other site 358220013221 Q-loop/lid; other site 358220013222 ABC transporter signature motif; other site 358220013223 Walker B; other site 358220013224 D-loop; other site 358220013225 H-loop/switch region; other site 358220013226 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 358220013227 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220013228 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 358220013229 TM-ABC transporter signature motif; other site 358220013230 Transcriptional regulators [Transcription]; Region: PurR; COG1609 358220013231 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 358220013232 DNA binding site [nucleotide binding] 358220013233 domain linker motif; other site 358220013234 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 358220013235 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 358220013236 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 358220013237 substrate binding site [chemical binding]; other site 358220013238 dimer interface [polypeptide binding]; other site 358220013239 ATP binding site [chemical binding]; other site 358220013240 D-ribose pyranase; Provisional; Region: PRK11797 358220013241 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 358220013242 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 358220013243 lytic murein transglycosylase; Provisional; Region: PRK11619 358220013244 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 358220013245 N-acetyl-D-glucosamine binding site [chemical binding]; other site 358220013246 catalytic residue [active] 358220013247 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 358220013248 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 358220013249 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220013250 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 358220013251 putative C-terminal domain interface [polypeptide binding]; other site 358220013252 putative GSH binding site (G-site) [chemical binding]; other site 358220013253 putative dimer interface [polypeptide binding]; other site 358220013254 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 358220013255 putative N-terminal domain interface [polypeptide binding]; other site 358220013256 putative dimer interface [polypeptide binding]; other site 358220013257 putative substrate binding pocket (H-site) [chemical binding]; other site 358220013258 NIPSNAP; Region: NIPSNAP; pfam07978 358220013259 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 358220013260 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 358220013261 active site 358220013262 NTP binding site [chemical binding]; other site 358220013263 metal binding triad [ion binding]; metal-binding site 358220013264 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 358220013265 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220013266 Zn2+ binding site [ion binding]; other site 358220013267 Mg2+ binding site [ion binding]; other site 358220013268 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 358220013269 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220013270 Coenzyme A binding pocket [chemical binding]; other site 358220013271 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 358220013272 RNA polymerase sigma factor; Provisional; Region: PRK12536 358220013273 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220013274 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220013275 DNA binding residues [nucleotide binding] 358220013276 Predicted integral membrane protein (DUF2282); Region: DUF2282; pfam10048 358220013277 hypothetical protein; Provisional; Region: PRK05409 358220013278 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 358220013279 Predicted membrane protein [Function unknown]; Region: COG2259 358220013280 thioredoxin 2; Provisional; Region: PRK10996 358220013281 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 358220013282 catalytic residues [active] 358220013283 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220013284 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 358220013285 active site 358220013286 motif I; other site 358220013287 motif II; other site 358220013288 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 358220013289 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 358220013290 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 358220013291 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 358220013292 active site 358220013293 homotetramer interface [polypeptide binding]; other site 358220013294 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 358220013295 Uncharacterized conserved protein [Function unknown]; Region: COG1565 358220013296 short chain dehydrogenase; Provisional; Region: PRK09134 358220013297 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220013298 NAD(P) binding site [chemical binding]; other site 358220013299 active site 358220013300 Dihydroneopterin aldolase; Region: FolB; smart00905 358220013301 active site 358220013302 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 358220013303 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 358220013304 NAD(P) binding site [chemical binding]; other site 358220013305 catalytic residues [active] 358220013306 short chain dehydrogenase; Provisional; Region: PRK12939 358220013307 classical (c) SDRs; Region: SDR_c; cd05233 358220013308 NAD(P) binding site [chemical binding]; other site 358220013309 active site 358220013310 DctM-like transporters; Region: DctM; pfam06808 358220013311 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 358220013312 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 358220013313 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220013314 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 358220013315 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220013316 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220013317 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 358220013318 Helix-turn-helix domain; Region: HTH_18; pfam12833 358220013319 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 358220013320 Protein of unknown function (DUF2390); Region: DUF2390; pfam09523 358220013321 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 358220013322 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 358220013323 substrate binding site [chemical binding]; other site 358220013324 oxyanion hole (OAH) forming residues; other site 358220013325 trimer interface [polypeptide binding]; other site 358220013326 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 358220013327 Flavoprotein; Region: Flavoprotein; pfam02441 358220013328 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; pfam01977 358220013329 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 358220013330 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 358220013331 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 358220013332 acyl-activating enzyme (AAE) consensus motif; other site 358220013333 acyl-activating enzyme (AAE) consensus motif; other site 358220013334 putative AMP binding site [chemical binding]; other site 358220013335 putative active site [active] 358220013336 putative CoA binding site [chemical binding]; other site 358220013337 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 358220013338 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220013339 catalytic loop [active] 358220013340 iron binding site [ion binding]; other site 358220013341 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 358220013342 FAD binding domain in molybdopterin dehydrogenase; Region: FAD_binding_5; pfam00941 358220013343 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 358220013344 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 358220013345 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 358220013346 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 358220013347 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 358220013348 putative hydrophobic ligand binding site [chemical binding]; other site 358220013349 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220013350 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220013351 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220013352 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220013353 dimerization interface [polypeptide binding]; other site 358220013354 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 358220013355 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 358220013356 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 358220013357 Ligand Binding Site [chemical binding]; other site 358220013358 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 358220013359 catalytic core [active] 358220013360 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 358220013361 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 358220013362 dimer interface [polypeptide binding]; other site 358220013363 active site 358220013364 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 358220013365 substrate binding site [chemical binding]; other site 358220013366 catalytic residue [active] 358220013367 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 358220013368 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 358220013369 YhhN-like protein; Region: YhhN; pfam07947 358220013370 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 358220013371 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220013372 Walker A motif; other site 358220013373 ATP binding site [chemical binding]; other site 358220013374 Walker B motif; other site 358220013375 arginine finger; other site 358220013376 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 358220013377 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 358220013378 active site 358220013379 zinc binding site [ion binding]; other site 358220013380 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 358220013381 RuvA N terminal domain; Region: RuvA_N; pfam01330 358220013382 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 358220013383 PhoH-like protein; Region: PhoH; pfam02562 358220013384 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 358220013385 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 358220013386 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220013387 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 358220013388 Ligand Binding Site [chemical binding]; other site 358220013389 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 358220013390 putative active site [active] 358220013391 dimerization interface [polypeptide binding]; other site 358220013392 putative tRNAtyr binding site [nucleotide binding]; other site 358220013393 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 358220013394 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 358220013395 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220013396 dimer interface [polypeptide binding]; other site 358220013397 phosphorylation site [posttranslational modification] 358220013398 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220013399 Mg2+ binding site [ion binding]; other site 358220013400 G-X-G motif; other site 358220013401 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 358220013402 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013403 active site 358220013404 phosphorylation site [posttranslational modification] 358220013405 intermolecular recognition site; other site 358220013406 dimerization interface [polypeptide binding]; other site 358220013407 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220013408 DNA binding residues [nucleotide binding] 358220013409 dimerization interface [polypeptide binding]; other site 358220013410 Domain of unknown function (DUF336); Region: DUF336; cl01249 358220013411 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 358220013412 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 358220013413 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 358220013414 Transposase domain (DUF772); Region: DUF772; pfam05598 358220013415 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 358220013416 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 358220013417 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 358220013418 trimer interface [polypeptide binding]; other site 358220013419 eyelet of channel; other site 358220013420 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 358220013421 CoA-transferase family III; Region: CoA_transf_3; pfam02515 358220013422 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220013423 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 358220013424 Lignostilbene-alpha,beta-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3670 358220013425 Retinal pigment epithelial membrane protein; Region: RPE65; pfam03055 358220013426 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 358220013427 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 358220013428 dimer interface [polypeptide binding]; other site 358220013429 active site 358220013430 Predicted transcriptional regulators [Transcription]; Region: COG1733 358220013431 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 358220013432 Predicted transcriptional regulators [Transcription]; Region: COG1733 358220013433 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 358220013434 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 358220013435 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 358220013436 ATP binding site [chemical binding]; other site 358220013437 Mg++ binding site [ion binding]; other site 358220013438 motif III; other site 358220013439 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220013440 nucleotide binding region [chemical binding]; other site 358220013441 ATP-binding site [chemical binding]; other site 358220013442 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 358220013443 putative RNA binding site [nucleotide binding]; other site 358220013444 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 358220013445 PAS fold; Region: PAS_4; pfam08448 358220013446 PAS domain S-box; Region: sensory_box; TIGR00229 358220013447 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220013448 putative active site [active] 358220013449 heme pocket [chemical binding]; other site 358220013450 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220013451 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220013452 metal binding site [ion binding]; metal-binding site 358220013453 active site 358220013454 I-site; other site 358220013455 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220013456 AMP nucleosidase; Provisional; Region: PRK08292 358220013457 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 358220013458 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 358220013459 Creatinine amidohydrolase; Region: Creatininase; pfam02633 358220013460 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 358220013461 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 358220013462 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 358220013463 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 358220013464 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 358220013465 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 358220013466 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 358220013467 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 358220013468 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 358220013469 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 358220013470 DsbD alpha interface [polypeptide binding]; other site 358220013471 catalytic residues [active] 358220013472 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 358220013473 putative catalytic residue [active] 358220013474 CoA binding domain; Region: CoA_binding; cl17356 358220013475 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 358220013476 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 358220013477 homodimer interface [polypeptide binding]; other site 358220013478 substrate-cofactor binding pocket; other site 358220013479 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220013480 catalytic residue [active] 358220013481 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 358220013482 Transcriptional regulator [Transcription]; Region: IclR; COG1414 358220013483 Bacterial transcriptional regulator; Region: IclR; pfam01614 358220013484 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 358220013485 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 358220013486 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220013487 Protein of unknown function (DUF2783); Region: DUF2783; pfam10932 358220013488 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220013489 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 358220013490 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 358220013491 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 358220013492 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220013493 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220013494 dimerization interface [polypeptide binding]; other site 358220013495 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 358220013496 Sulfatase; Region: Sulfatase; pfam00884 358220013497 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 358220013498 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 358220013499 MarR family; Region: MarR_2; pfam12802 358220013500 Transmembrane secretion effector; Region: MFS_3; pfam05977 358220013501 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220013502 putative substrate translocation pore; other site 358220013503 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 358220013504 substrate binding site [chemical binding]; other site 358220013505 active site 358220013506 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 358220013507 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl17194 358220013508 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl17194 358220013509 primosome assembly protein PriA; Validated; Region: PRK05580 358220013510 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220013511 ATP binding site [chemical binding]; other site 358220013512 putative Mg++ binding site [ion binding]; other site 358220013513 helicase superfamily c-terminal domain; Region: HELICc; smart00490 358220013514 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 358220013515 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 358220013516 Cupin domain; Region: Cupin_2; cl17218 358220013517 Predicted permeases [General function prediction only]; Region: COG0679 358220013518 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 358220013519 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_2; cd06335 358220013520 putative ligand binding site [chemical binding]; other site 358220013521 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 358220013522 Part of AAA domain; Region: AAA_19; pfam13245 358220013523 Family description; Region: UvrD_C_2; pfam13538 358220013524 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 358220013525 substrate binding site [chemical binding]; other site 358220013526 dimerization interface [polypeptide binding]; other site 358220013527 active site 358220013528 calcium binding site [ion binding]; other site 358220013529 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 358220013530 Ligand Binding Site [chemical binding]; other site 358220013531 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 358220013532 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 358220013533 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220013534 PAS domain; Region: PAS_9; pfam13426 358220013535 putative active site [active] 358220013536 heme pocket [chemical binding]; other site 358220013537 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220013538 DNA binding residues [nucleotide binding] 358220013539 dimerization interface [polypeptide binding]; other site 358220013540 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220013541 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220013542 metal binding site [ion binding]; metal-binding site 358220013543 active site 358220013544 I-site; other site 358220013545 Double zinc ribbon; Region: DZR; pfam12773 358220013546 Uncharacterized protein conserved in bacteria (DUF2145); Region: DUF2145; pfam09916 358220013547 yiaA/B two helix domain; Region: YiaAB; cl01759 358220013548 yiaA/B two helix domain; Region: YiaAB; cl01759 358220013549 Uncharacterized conserved protein [Function unknown]; Region: COG3268 358220013550 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220013551 NAD(P) binding site [chemical binding]; other site 358220013552 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 358220013553 EamA-like transporter family; Region: EamA; pfam00892 358220013554 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220013555 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 358220013556 AsnC family; Region: AsnC_trans_reg; pfam01037 358220013557 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 358220013558 Aminocyclopropane-1-carboxylate deaminase (ACCD): Pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of 1-aminocyclopropane-L-carboxylate (ACC), a precursor of the plant hormone ethylene, to alpha-ketobutyrate and ammonia; Region: ACCD; cd06449 358220013559 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220013560 catalytic residue [active] 358220013561 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220013562 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 358220013563 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 358220013564 putative acyl-acceptor binding pocket; other site 358220013565 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 358220013566 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220013567 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220013568 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 358220013569 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 358220013570 ABC1 family; Region: ABC1; cl17513 358220013571 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 358220013572 active site 358220013573 ATP binding site [chemical binding]; other site 358220013574 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 358220013575 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 358220013576 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 358220013577 hydroxyglutarate oxidase; Provisional; Region: PRK11728 358220013578 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 358220013579 sulfite oxidase; Provisional; Region: PLN00177 358220013580 Subgroup of sulfite oxidase (SO) family molybdopterin binding domains that contains conserved dimerization domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate...; Region: SO_family_Moco_dimer; cd02110 358220013581 Moco binding site; other site 358220013582 metal coordination site [ion binding]; other site 358220013583 dimerization interface [polypeptide binding]; other site 358220013584 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 358220013585 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 358220013586 active site residue [active] 358220013587 Domain of unknown function DUF21; Region: DUF21; pfam01595 358220013588 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 358220013589 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 358220013590 Transporter associated domain; Region: CorC_HlyC; smart01091 358220013591 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4398 358220013592 FIST N domain; Region: FIST; smart00897 358220013593 FIST C domain; Region: FIST_C; pfam10442 358220013594 Protein of unknown function (DUF461); Region: DUF461; pfam04314 358220013595 Reeler-like domain of YcnI and similar proteins; Region: YcnI_like; cd08545 358220013596 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 358220013597 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 358220013598 N-terminal plug; other site 358220013599 ligand-binding site [chemical binding]; other site 358220013600 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220013601 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 358220013602 C-terminal domain interface [polypeptide binding]; other site 358220013603 GSH binding site (G-site) [chemical binding]; other site 358220013604 dimer interface [polypeptide binding]; other site 358220013605 C-terminal, alpha helical domain of an unknown subfamily 9 of Glutathione S-transferases; Region: GST_C_9; cd10424 358220013606 putative N-terminal domain interface [polypeptide binding]; other site 358220013607 putative dimer interface [polypeptide binding]; other site 358220013608 putative substrate binding pocket (H-site) [chemical binding]; other site 358220013609 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 358220013610 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220013611 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_18; cd08357 358220013612 putative metal binding site [ion binding]; other site 358220013613 MarC family integral membrane protein; Region: MarC; cl00919 358220013614 Transcriptional regulator; Region: Rrf2; cl17282 358220013615 Rrf2 family protein; Region: rrf2_super; TIGR00738 358220013616 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 358220013617 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220013618 The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; Region: PBP2_NhaR; cd08429 358220013619 putative dimerization interface [polypeptide binding]; other site 358220013620 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 358220013621 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 358220013622 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 358220013623 alphaNTD homodimer interface [polypeptide binding]; other site 358220013624 alphaNTD - beta interaction site [polypeptide binding]; other site 358220013625 alphaNTD - beta' interaction site [polypeptide binding]; other site 358220013626 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 358220013627 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 358220013628 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 358220013629 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 358220013630 RNA binding surface [nucleotide binding]; other site 358220013631 30S ribosomal protein S11; Validated; Region: PRK05309 358220013632 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 358220013633 30S ribosomal protein S13; Region: bact_S13; TIGR03631 358220013634 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 358220013635 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 358220013636 SecY translocase; Region: SecY; pfam00344 358220013637 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 358220013638 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 358220013639 23S rRNA binding site [nucleotide binding]; other site 358220013640 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 358220013641 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 358220013642 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 358220013643 Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA...; Region: Ribosomal_L18_L5e; cd00432 358220013644 5S rRNA interface [nucleotide binding]; other site 358220013645 23S rRNA interface [nucleotide binding]; other site 358220013646 L5 interface [polypeptide binding]; other site 358220013647 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 358220013648 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 358220013649 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 358220013650 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 358220013651 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 358220013652 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 358220013653 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 358220013654 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 358220013655 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 358220013656 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 358220013657 RNA binding site [nucleotide binding]; other site 358220013658 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 358220013659 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 358220013660 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 358220013661 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 358220013662 Predicted small integral membrane protein (DUF2160); Region: DUF2160; pfam09928 358220013663 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 358220013664 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 358220013665 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220013666 dimer interface [polypeptide binding]; other site 358220013667 conserved gate region; other site 358220013668 putative PBP binding loops; other site 358220013669 ABC-ATPase subunit interface; other site 358220013670 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 358220013671 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 358220013672 putative PBP binding loops; other site 358220013673 ABC-ATPase subunit interface; other site 358220013674 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 358220013675 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 358220013676 Walker A/P-loop; other site 358220013677 ATP binding site [chemical binding]; other site 358220013678 Q-loop/lid; other site 358220013679 ABC transporter signature motif; other site 358220013680 Walker B; other site 358220013681 D-loop; other site 358220013682 H-loop/switch region; other site 358220013683 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 358220013684 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 358220013685 Walker A/P-loop; other site 358220013686 ATP binding site [chemical binding]; other site 358220013687 Q-loop/lid; other site 358220013688 ABC transporter signature motif; other site 358220013689 Walker B; other site 358220013690 D-loop; other site 358220013691 H-loop/switch region; other site 358220013692 TOBE domain; Region: TOBE_2; pfam08402 358220013693 DNA-binding transcriptional activator FucR; Provisional; Region: PRK10411 358220013694 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 358220013695 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 358220013696 glycerol kinase; Provisional; Region: glpK; PRK00047 358220013697 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 358220013698 N- and C-terminal domain interface [polypeptide binding]; other site 358220013699 active site 358220013700 MgATP binding site [chemical binding]; other site 358220013701 catalytic site [active] 358220013702 metal binding site [ion binding]; metal-binding site 358220013703 glycerol binding site [chemical binding]; other site 358220013704 homotetramer interface [polypeptide binding]; other site 358220013705 homodimer interface [polypeptide binding]; other site 358220013706 FBP binding site [chemical binding]; other site 358220013707 protein IIAGlc interface [polypeptide binding]; other site 358220013708 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 358220013709 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 358220013710 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 358220013711 UbiA prenyltransferase family; Region: UbiA; pfam01040 358220013712 CHASE3 domain; Region: CHASE3; pfam05227 358220013713 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220013714 GAF domain; Region: GAF; pfam01590 358220013715 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220013716 dimer interface [polypeptide binding]; other site 358220013717 phosphorylation site [posttranslational modification] 358220013718 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220013719 ATP binding site [chemical binding]; other site 358220013720 Mg2+ binding site [ion binding]; other site 358220013721 G-X-G motif; other site 358220013722 Response regulator receiver domain; Region: Response_reg; pfam00072 358220013723 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013724 active site 358220013725 phosphorylation site [posttranslational modification] 358220013726 intermolecular recognition site; other site 358220013727 dimerization interface [polypeptide binding]; other site 358220013728 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220013729 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013730 active site 358220013731 phosphorylation site [posttranslational modification] 358220013732 intermolecular recognition site; other site 358220013733 dimerization interface [polypeptide binding]; other site 358220013734 Response regulator receiver domain; Region: Response_reg; pfam00072 358220013735 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013736 active site 358220013737 phosphorylation site [posttranslational modification] 358220013738 intermolecular recognition site; other site 358220013739 dimerization interface [polypeptide binding]; other site 358220013740 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 358220013741 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 358220013742 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 358220013743 CheB methylesterase; Region: CheB_methylest; pfam01339 358220013744 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013745 Response regulator receiver domain; Region: Response_reg; pfam00072 358220013746 active site 358220013747 phosphorylation site [posttranslational modification] 358220013748 intermolecular recognition site; other site 358220013749 dimerization interface [polypeptide binding]; other site 358220013750 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220013751 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220013752 dimer interface [polypeptide binding]; other site 358220013753 phosphorylation site [posttranslational modification] 358220013754 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220013755 ATP binding site [chemical binding]; other site 358220013756 Mg2+ binding site [ion binding]; other site 358220013757 G-X-G motif; other site 358220013758 Response regulator receiver domain; Region: Response_reg; pfam00072 358220013759 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013760 active site 358220013761 phosphorylation site [posttranslational modification] 358220013762 intermolecular recognition site; other site 358220013763 dimerization interface [polypeptide binding]; other site 358220013764 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 358220013765 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 358220013766 dimerization interface [polypeptide binding]; other site 358220013767 DPS ferroxidase diiron center [ion binding]; other site 358220013768 ion pore; other site 358220013769 hypothetical protein; Provisional; Region: PRK06156 358220013770 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 358220013771 active site 358220013772 metal binding site [ion binding]; metal-binding site 358220013773 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 358220013774 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220013775 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 358220013776 dimerization interface [polypeptide binding]; other site 358220013777 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 358220013778 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 358220013779 generic binding surface II; other site 358220013780 ssDNA binding site; other site 358220013781 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 358220013782 ATP binding site [chemical binding]; other site 358220013783 putative Mg++ binding site [ion binding]; other site 358220013784 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 358220013785 nucleotide binding region [chemical binding]; other site 358220013786 ATP-binding site [chemical binding]; other site 358220013787 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 358220013788 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 358220013789 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220013790 Zn2+ binding site [ion binding]; other site 358220013791 Mg2+ binding site [ion binding]; other site 358220013792 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 358220013793 putative substrate binding site [chemical binding]; other site 358220013794 putative ATP binding site [chemical binding]; other site 358220013795 Queuosine biosynthesis protein; Region: Queuosine_synth; pfam02547 358220013796 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 358220013797 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220013798 EamA-like transporter family; Region: EamA; pfam00892 358220013799 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 358220013800 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 358220013801 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220013802 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220013803 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220013804 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_5; cd08426 358220013805 putative dimerization interface [polypeptide binding]; other site 358220013806 Protein of unknown function (DUF3253); Region: DUF3253; pfam11625 358220013807 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 358220013808 ligand binding site [chemical binding]; other site 358220013809 active site 358220013810 UGI interface [polypeptide binding]; other site 358220013811 catalytic site [active] 358220013812 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 358220013813 active site 358220013814 ribulose/triose binding site [chemical binding]; other site 358220013815 phosphate binding site [ion binding]; other site 358220013816 substrate (anthranilate) binding pocket [chemical binding]; other site 358220013817 product (indole) binding pocket [chemical binding]; other site 358220013818 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 358220013819 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 358220013820 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 358220013821 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 358220013822 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 358220013823 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 358220013824 glutamine binding [chemical binding]; other site 358220013825 catalytic triad [active] 358220013826 Chorismate mutase type II; Region: CM_2; smart00830 358220013827 anthranilate synthase component I; Provisional; Region: PRK13565 358220013828 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 358220013829 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 358220013830 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 358220013831 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 358220013832 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220013833 dimerization interface [polypeptide binding]; other site 358220013834 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220013835 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220013836 dimer interface [polypeptide binding]; other site 358220013837 putative CheW interface [polypeptide binding]; other site 358220013838 phosphoglycolate phosphatase; Provisional; Region: PRK13222 358220013839 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220013840 motif II; other site 358220013841 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 358220013842 SPFH domain / Band 7 family; Region: Band_7; pfam01145 358220013843 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220013844 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013845 active site 358220013846 phosphorylation site [posttranslational modification] 358220013847 intermolecular recognition site; other site 358220013848 dimerization interface [polypeptide binding]; other site 358220013849 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cl17355 358220013850 DNA binding site [nucleotide binding] 358220013851 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220013852 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220013853 ATP binding site [chemical binding]; other site 358220013854 Mg2+ binding site [ion binding]; other site 358220013855 G-X-G motif; other site 358220013856 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 358220013857 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 358220013858 substrate binding site [chemical binding]; other site 358220013859 hexamer interface [polypeptide binding]; other site 358220013860 metal binding site [ion binding]; metal-binding site 358220013861 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 358220013862 Site-specific recombinase; Region: SpecificRecomb; pfam10136 358220013863 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 358220013864 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 358220013865 thiamine monophosphate kinase; Provisional; Region: PRK05731 358220013866 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 358220013867 ATP binding site [chemical binding]; other site 358220013868 dimerization interface [polypeptide binding]; other site 358220013869 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 358220013870 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 358220013871 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 358220013872 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 358220013873 DNA binding residues [nucleotide binding] 358220013874 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 358220013875 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 358220013876 FAD binding pocket [chemical binding]; other site 358220013877 FAD binding motif [chemical binding]; other site 358220013878 phosphate binding motif [ion binding]; other site 358220013879 beta-alpha-beta structure motif; other site 358220013880 NAD binding pocket [chemical binding]; other site 358220013881 hypothetical protein; Provisional; Region: PRK07877 358220013882 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220013883 NAD(P) binding site [chemical binding]; other site 358220013884 active site 358220013885 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 358220013886 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220013887 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220013888 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220013889 putative effector binding pocket; other site 358220013890 dimerization interface [polypeptide binding]; other site 358220013891 conserved hypothetical protein; Region: TIGR02231 358220013892 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 358220013893 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 358220013894 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 358220013895 Ligand Binding Site [chemical binding]; other site 358220013896 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 358220013897 tetramer interfaces [polypeptide binding]; other site 358220013898 binuclear metal-binding site [ion binding]; other site 358220013899 Competence-damaged protein; Region: CinA; pfam02464 358220013900 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 358220013901 SnoaL-like domain; Region: SnoaL_2; pfam12680 358220013902 Uncharacterized protein family (UPF0149); Region: UPF0149; pfam03695 358220013903 SEC-C motif; Region: SEC-C; pfam02810 358220013904 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 358220013905 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 358220013906 active site 358220013907 FMN binding site [chemical binding]; other site 358220013908 substrate binding site [chemical binding]; other site 358220013909 3Fe-4S cluster binding site [ion binding]; other site 358220013910 CcdB protein; Region: CcdB; cl03380 358220013911 Post-segregation antitoxin CcdA; Region: CcdA; cl02188 358220013912 PIN domain; Region: PIN_3; pfam13470 358220013913 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 358220013914 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 358220013915 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 358220013916 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 358220013917 active site 358220013918 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 358220013919 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 358220013920 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 358220013921 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 358220013922 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 358220013923 Walker A/P-loop; other site 358220013924 ATP binding site [chemical binding]; other site 358220013925 Q-loop/lid; other site 358220013926 ABC transporter signature motif; other site 358220013927 Walker B; other site 358220013928 D-loop; other site 358220013929 H-loop/switch region; other site 358220013930 OstA-like protein; Region: OstA; pfam03968 358220013931 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 358220013932 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 358220013933 catalytic residues [active] 358220013934 hinge region; other site 358220013935 alpha helical domain; other site 358220013936 Sporulation related domain; Region: SPOR; pfam05036 358220013937 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 358220013938 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 358220013939 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 358220013940 active site 358220013941 HIGH motif; other site 358220013942 nucleotide binding site [chemical binding]; other site 358220013943 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 358220013944 KMSK motif region; other site 358220013945 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 358220013946 tRNA binding surface [nucleotide binding]; other site 358220013947 anticodon binding site; other site 358220013948 psiF repeat; Region: PsiF_repeat; pfam07769 358220013949 psiF repeat; Region: PsiF_repeat; pfam07769 358220013950 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 358220013951 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 358220013952 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 358220013953 PAS domain; Region: PAS; smart00091 358220013954 PAS fold; Region: PAS_7; pfam12860 358220013955 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220013956 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220013957 dimer interface [polypeptide binding]; other site 358220013958 phosphorylation site [posttranslational modification] 358220013959 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220013960 ATP binding site [chemical binding]; other site 358220013961 Mg2+ binding site [ion binding]; other site 358220013962 G-X-G motif; other site 358220013963 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013964 Response regulator receiver domain; Region: Response_reg; pfam00072 358220013965 active site 358220013966 phosphorylation site [posttranslational modification] 358220013967 intermolecular recognition site; other site 358220013968 dimerization interface [polypeptide binding]; other site 358220013969 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 358220013970 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220013971 active site 358220013972 phosphorylation site [posttranslational modification] 358220013973 intermolecular recognition site; other site 358220013974 dimerization interface [polypeptide binding]; other site 358220013975 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220013976 DNA binding residues [nucleotide binding] 358220013977 dimerization interface [polypeptide binding]; other site 358220013978 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220013979 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220013980 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220013981 putative effector binding pocket; other site 358220013982 dimerization interface [polypeptide binding]; other site 358220013983 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 358220013984 Coenzyme A transferase; Region: CoA_trans; smart00882 358220013985 Coenzyme A transferase; Region: CoA_trans; cl17247 358220013986 Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate...; Region: malate_synt_G; cd00728 358220013987 active site 358220013988 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 358220013989 4-oxalocrotonate tautomerase; Provisional; Region: PRK00745 358220013990 active site 1 [active] 358220013991 dimer interface [polypeptide binding]; other site 358220013992 hexamer interface [polypeptide binding]; other site 358220013993 active site 2 [active] 358220013994 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220013995 putative substrate translocation pore; other site 358220013996 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220013997 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 358220013998 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 358220013999 putative active site [active] 358220014000 putative dimer interface [polypeptide binding]; other site 358220014001 glutathione synthetase; Provisional; Region: PRK05246 358220014002 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 358220014003 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 358220014004 Benzoate membrane transport protein; Region: BenE; pfam03594 358220014005 benzoate transporter; Region: benE; TIGR00843 358220014006 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 358220014007 potassium uptake protein; Region: kup; TIGR00794 358220014008 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 358220014009 Glutamate-cysteine ligase; Region: GshA; pfam08886 358220014010 Cation transport protein; Region: TrkH; cl17365 358220014011 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 358220014012 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 358220014013 TrkA-N domain; Region: TrkA_N; pfam02254 358220014014 TrkA-C domain; Region: TrkA_C; pfam02080 358220014015 TrkA-N domain; Region: TrkA_N; pfam02254 358220014016 TrkA-C domain; Region: TrkA_C; pfam02080 358220014017 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 358220014018 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 358220014019 putative catalytic cysteine [active] 358220014020 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 358220014021 FAD dependent oxidoreductase; Region: DAO; pfam01266 358220014022 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 358220014023 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 358220014024 Arginase family; Region: Arginase; cd09989 358220014025 agmatinase; Region: agmatinase; TIGR01230 358220014026 active site 358220014027 Mn binding site [ion binding]; other site 358220014028 oligomer interface [polypeptide binding]; other site 358220014029 Lipopolysaccharide-assembly; Region: LptE; pfam04390 358220014030 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 358220014031 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 358220014032 HIGH motif; other site 358220014033 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 358220014034 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 358220014035 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 358220014036 active site 358220014037 KMSKS motif; other site 358220014038 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 358220014039 tRNA binding surface [nucleotide binding]; other site 358220014040 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 358220014041 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 358220014042 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 358220014043 dihydrodipicolinate reductase; Provisional; Region: PRK00048 358220014044 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 358220014045 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 358220014046 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 358220014047 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 358220014048 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 358220014049 ferric uptake regulator; Provisional; Region: fur; PRK09462 358220014050 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 358220014051 metal binding site 2 [ion binding]; metal-binding site 358220014052 putative DNA binding helix; other site 358220014053 metal binding site 1 [ion binding]; metal-binding site 358220014054 dimer interface [polypeptide binding]; other site 358220014055 structural Zn2+ binding site [ion binding]; other site 358220014056 HPr kinase/phosphorylase; Provisional; Region: PRK05428 358220014057 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 358220014058 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 358220014059 Hpr binding site; other site 358220014060 active site 358220014061 homohexamer subunit interaction site [polypeptide binding]; other site 358220014062 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 358220014063 active site 358220014064 phosphorylation site [posttranslational modification] 358220014065 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 358220014066 30S subunit binding site; other site 358220014067 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 358220014068 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220014069 putative substrate translocation pore; other site 358220014070 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 358220014071 active site 358220014072 ATP binding site [chemical binding]; other site 358220014073 substrate binding site [chemical binding]; other site 358220014074 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 358220014075 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 358220014076 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 358220014077 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 358220014078 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 358220014079 ATP-grasp domain; Region: ATP-grasp; pfam02222 358220014080 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 358220014081 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 358220014082 Triacylglycerol lipase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: Triacylglycerol_lipase_like; cd01847 358220014083 active site 358220014084 catalytic triad [active] 358220014085 oxyanion hole [active] 358220014086 Homeodomain-like domain; Region: HTH_23; cl17451 358220014087 putative transposase OrfB; Reviewed; Region: PHA02517 358220014088 Integrase core domain; Region: rve; pfam00665 358220014089 Integrase core domain; Region: rve_3; pfam13683 358220014090 OmpW family; Region: OmpW; cl17427 358220014091 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 358220014092 active site 358220014093 catalytic triad [active] 358220014094 oxyanion hole [active] 358220014095 Secretory lipase; Region: LIP; pfam03583 358220014096 Uncharacterized conserved protein [Function unknown]; Region: COG4095 358220014097 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 358220014098 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 358220014099 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 358220014100 Glycoprotease family; Region: Peptidase_M22; pfam00814 358220014101 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 358220014102 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220014103 Coenzyme A binding pocket [chemical binding]; other site 358220014104 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 358220014105 active site 358220014106 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 358220014107 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 358220014108 Cl binding site [ion binding]; other site 358220014109 oligomer interface [polypeptide binding]; other site 358220014110 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 358220014111 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 358220014112 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 358220014113 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 358220014114 acyl-activating enzyme (AAE) consensus motif; other site 358220014115 putative AMP binding site [chemical binding]; other site 358220014116 putative active site [active] 358220014117 putative CoA binding site [chemical binding]; other site 358220014118 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 358220014119 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 358220014120 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 358220014121 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 358220014122 ligand binding site [chemical binding]; other site 358220014123 homodimer interface [polypeptide binding]; other site 358220014124 NAD(P) binding site [chemical binding]; other site 358220014125 trimer interface B [polypeptide binding]; other site 358220014126 trimer interface A [polypeptide binding]; other site 358220014127 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 358220014128 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 358220014129 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 358220014130 intersubunit interface [polypeptide binding]; other site 358220014131 active site 358220014132 zinc binding site [ion binding]; other site 358220014133 Na+ binding site [ion binding]; other site 358220014134 sensor protein QseC; Provisional; Region: PRK10337 358220014135 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 358220014136 Mg2+ binding site [ion binding]; other site 358220014137 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220014138 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220014139 active site 358220014140 phosphorylation site [posttranslational modification] 358220014141 intermolecular recognition site; other site 358220014142 dimerization interface [polypeptide binding]; other site 358220014143 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220014144 DNA binding site [nucleotide binding] 358220014145 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 358220014146 active site 358220014147 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 358220014148 active site 358220014149 pyruvate kinase; Provisional; Region: PRK05826 358220014150 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 358220014151 domain interfaces; other site 358220014152 active site 358220014153 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 358220014154 proline aminopeptidase P II; Provisional; Region: PRK10879 358220014155 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 358220014156 active site 358220014157 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 358220014158 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 358220014159 Substrate binding site; other site 358220014160 metal-binding site 358220014161 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; pfam02675 358220014162 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 358220014163 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 358220014164 TPP-binding site [chemical binding]; other site 358220014165 dimer interface [polypeptide binding]; other site 358220014166 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 358220014167 PYR/PP interface [polypeptide binding]; other site 358220014168 dimer interface [polypeptide binding]; other site 358220014169 TPP binding site [chemical binding]; other site 358220014170 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 358220014171 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 358220014172 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 358220014173 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 358220014174 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 358220014175 Mechanosensitive ion channel; Region: MS_channel; pfam00924 358220014176 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 358220014177 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 358220014178 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 358220014179 ligand binding site [chemical binding]; other site 358220014180 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 358220014181 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 358220014182 active site 358220014183 catalytic tetrad [active] 358220014184 hypothetical protein; Provisional; Region: PRK07538 358220014185 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 358220014186 ATP-dependent Clp protease proteolytic subunit; Reviewed; Region: PRK12553 358220014187 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 358220014188 oligomer interface [polypeptide binding]; other site 358220014189 active site residues [active] 358220014190 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 358220014191 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 358220014192 Subunit B of the Class III extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of protocatechuate; Region: PCA_45_Dioxygenase_B; cd07364 358220014193 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 358220014194 active site 358220014195 Fe(II) binding site [ion binding]; other site 358220014196 dimer interface [polypeptide binding]; other site 358220014197 tetramer interface [polypeptide binding]; other site 358220014198 The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit; Region: PCA_45_Doxase_A; cd07924 358220014199 tetramer interface [polypeptide binding]; other site 358220014200 dimer interface [polypeptide binding]; other site 358220014201 active site 358220014202 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 358220014203 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 358220014204 active site 358220014205 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220014206 hypothetical protein; Provisional; Region: PRK09262 358220014207 Amidohydrolase; Region: Amidohydro_2; pfam04909 358220014208 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 358220014209 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 358220014210 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014211 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 358220014212 putative dimerization interface [polypeptide binding]; other site 358220014213 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 358220014214 Domain of unknown function (DUF1932); Region: DUF1932; pfam09130 358220014215 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220014216 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 358220014217 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 358220014218 Walker A/P-loop; other site 358220014219 ATP binding site [chemical binding]; other site 358220014220 Q-loop/lid; other site 358220014221 ABC transporter signature motif; other site 358220014222 Walker B; other site 358220014223 D-loop; other site 358220014224 H-loop/switch region; other site 358220014225 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 358220014226 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 358220014227 Walker A/P-loop; other site 358220014228 ATP binding site [chemical binding]; other site 358220014229 Q-loop/lid; other site 358220014230 ABC transporter signature motif; other site 358220014231 Walker B; other site 358220014232 D-loop; other site 358220014233 H-loop/switch region; other site 358220014234 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 358220014235 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 358220014236 TM-ABC transporter signature motif; other site 358220014237 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 358220014238 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 358220014239 TM-ABC transporter signature motif; other site 358220014240 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220014241 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 358220014242 Transcriptional regulators [Transcription]; Region: GntR; COG1802 358220014243 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 358220014244 DNA-binding site [nucleotide binding]; DNA binding site 358220014245 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 358220014246 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 358220014247 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 358220014248 iron-sulfur cluster [ion binding]; other site 358220014249 [2Fe-2S] cluster binding site [ion binding]; other site 358220014250 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 358220014251 alpha subunit interface [polypeptide binding]; other site 358220014252 active site 358220014253 substrate binding site [chemical binding]; other site 358220014254 Fe binding site [ion binding]; other site 358220014255 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 358220014256 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 358220014257 FMN-binding pocket [chemical binding]; other site 358220014258 flavin binding motif; other site 358220014259 phosphate binding motif [ion binding]; other site 358220014260 beta-alpha-beta structure motif; other site 358220014261 NAD binding pocket [chemical binding]; other site 358220014262 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 358220014263 catalytic loop [active] 358220014264 iron binding site [ion binding]; other site 358220014265 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cl00250 358220014266 30S subunit binding site; other site 358220014267 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 358220014268 Peptidase C26; Region: Peptidase_C26; pfam07722 358220014269 catalytic triad [active] 358220014270 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220014271 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014272 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 358220014273 substrate binding pocket [chemical binding]; other site 358220014274 dimerization interface [polypeptide binding]; other site 358220014275 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB); Region: LigA_like_1; cd07925 358220014276 putative dimer interface [polypeptide binding]; other site 358220014277 putative tetramer interface [polypeptide binding]; other site 358220014278 putative active site [active] 358220014279 The B subunit of unknown Class III extradiol dioxygenases with similarity to Protocatechuate 4,5-dioxygenase; Region: PCA_45_Doxase_B_like_1; cd07949 358220014280 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 358220014281 putative active site [active] 358220014282 Fe(II) binding site [ion binding]; other site 358220014283 putative dimer interface [polypeptide binding]; other site 358220014284 putative tetramer interface [polypeptide binding]; other site 358220014285 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]; Region: COG4277 358220014286 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 358220014287 FeS/SAM binding site; other site 358220014288 Domain of unknown function (DUF4130; Region: DUF4130; cl14836 358220014289 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 358220014290 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 358220014291 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220014292 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 358220014293 putative C-terminal domain interface [polypeptide binding]; other site 358220014294 putative GSH binding site (G-site) [chemical binding]; other site 358220014295 putative dimer interface [polypeptide binding]; other site 358220014296 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 358220014297 N-terminal domain interface [polypeptide binding]; other site 358220014298 dimer interface [polypeptide binding]; other site 358220014299 substrate binding pocket (H-site) [chemical binding]; other site 358220014300 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220014301 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014302 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_2; cd08471 358220014303 putative effector binding pocket; other site 358220014304 putative dimerization interface [polypeptide binding]; other site 358220014305 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 358220014306 Pirin-related protein [General function prediction only]; Region: COG1741 358220014307 Pirin; Region: Pirin; pfam02678 358220014308 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 358220014309 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 358220014310 Protein of unknown function (DUF1579); Region: DUF1579; pfam07617 358220014311 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 358220014312 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 358220014313 C-terminal domain interface [polypeptide binding]; other site 358220014314 GSH binding site (G-site) [chemical binding]; other site 358220014315 dimer interface [polypeptide binding]; other site 358220014316 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 358220014317 N-terminal domain interface [polypeptide binding]; other site 358220014318 dimer interface [polypeptide binding]; other site 358220014319 substrate binding pocket (H-site) [chemical binding]; other site 358220014320 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 358220014321 dimer interface [polypeptide binding]; other site 358220014322 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220014323 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 358220014324 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220014325 WHG domain; Region: WHG; pfam13305 358220014326 HTH domain; Region: HTH_11; pfam08279 358220014327 WYL domain; Region: WYL; pfam13280 358220014328 NIPSNAP; Region: NIPSNAP; pfam07978 358220014329 short chain dehydrogenase; Provisional; Region: PRK06180 358220014330 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 358220014331 NADP binding site [chemical binding]; other site 358220014332 active site 358220014333 steroid binding site; other site 358220014334 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220014335 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014336 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220014337 putative effector binding pocket; other site 358220014338 dimerization interface [polypeptide binding]; other site 358220014339 short chain dehydrogenase; Provisional; Region: PRK12937 358220014340 classical (c) SDRs; Region: SDR_c; cd05233 358220014341 NAD(P) binding site [chemical binding]; other site 358220014342 active site 358220014343 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014344 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220014345 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 358220014346 putative effector binding pocket; other site 358220014347 dimerization interface [polypeptide binding]; other site 358220014348 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 358220014349 aspartate racemase; Region: asp_race; TIGR00035 358220014350 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 358220014351 osmolarity response regulator; Provisional; Region: ompR; PRK09468 358220014352 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220014353 active site 358220014354 phosphorylation site [posttranslational modification] 358220014355 intermolecular recognition site; other site 358220014356 dimerization interface [polypeptide binding]; other site 358220014357 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220014358 DNA binding site [nucleotide binding] 358220014359 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 358220014360 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220014361 dimer interface [polypeptide binding]; other site 358220014362 phosphorylation site [posttranslational modification] 358220014363 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220014364 ATP binding site [chemical binding]; other site 358220014365 Mg2+ binding site [ion binding]; other site 358220014366 G-X-G motif; other site 358220014367 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 358220014368 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 358220014369 Walker A motif; other site 358220014370 ATP binding site [chemical binding]; other site 358220014371 Walker B motif; other site 358220014372 arginine finger; other site 358220014373 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 358220014374 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 358220014375 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 358220014376 NAD(P) binding site [chemical binding]; other site 358220014377 catalytic residues [active] 358220014378 Protein of unknown function (DUF779); Region: DUF779; pfam05610 358220014379 HAMP domain; Region: HAMP; pfam00672 358220014380 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220014381 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220014382 dimer interface [polypeptide binding]; other site 358220014383 putative CheW interface [polypeptide binding]; other site 358220014384 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 358220014385 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 358220014386 EamA-like transporter family; Region: EamA; pfam00892 358220014387 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 358220014388 active site 358220014389 Zn binding site [ion binding]; other site 358220014390 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 358220014391 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220014392 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014393 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220014394 dimerization interface [polypeptide binding]; other site 358220014395 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 358220014396 active site 358220014397 dimer interface [polypeptide binding]; other site 358220014398 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 358220014399 Phosphoglycerate kinase; Region: PGK; pfam00162 358220014400 substrate binding site [chemical binding]; other site 358220014401 hinge regions; other site 358220014402 ADP binding site [chemical binding]; other site 358220014403 catalytic site [active] 358220014404 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 358220014405 AzlC protein; Region: AzlC; pfam03591 358220014406 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 358220014407 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 358220014408 putative active site [active] 358220014409 substrate binding site [chemical binding]; other site 358220014410 putative cosubstrate binding site; other site 358220014411 catalytic site [active] 358220014412 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 358220014413 substrate binding site [chemical binding]; other site 358220014414 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 358220014415 active site 358220014416 catalytic residues [active] 358220014417 metal binding site [ion binding]; metal-binding site 358220014418 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 358220014419 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 358220014420 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 358220014421 DNA protecting protein DprA; Region: dprA; TIGR00732 358220014422 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 358220014423 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 358220014424 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 358220014425 Protein export membrane protein; Region: SecD_SecF; pfam02355 358220014426 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 358220014427 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 358220014428 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 358220014429 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 358220014430 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 358220014431 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 358220014432 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 358220014433 dimer interface [polypeptide binding]; other site 358220014434 PYR/PP interface [polypeptide binding]; other site 358220014435 TPP binding site [chemical binding]; other site 358220014436 substrate binding site [chemical binding]; other site 358220014437 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 358220014438 TPP-binding site; other site 358220014439 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 358220014440 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 358220014441 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 358220014442 putative DNA binding site [nucleotide binding]; other site 358220014443 putative Zn2+ binding site [ion binding]; other site 358220014444 AsnC family; Region: AsnC_trans_reg; pfam01037 358220014445 MltA specific insert domain; Region: MltA; smart00925 358220014446 3D domain; Region: 3D; pfam06725 358220014447 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 358220014448 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 358220014449 ligand binding site [chemical binding]; other site 358220014450 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 358220014451 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220014452 active site 358220014453 phosphorylation site [posttranslational modification] 358220014454 intermolecular recognition site; other site 358220014455 dimerization interface [polypeptide binding]; other site 358220014456 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 358220014457 DNA binding residues [nucleotide binding] 358220014458 dimerization interface [polypeptide binding]; other site 358220014459 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 358220014460 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220014461 putative active site [active] 358220014462 heme pocket [chemical binding]; other site 358220014463 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220014464 dimer interface [polypeptide binding]; other site 358220014465 phosphorylation site [posttranslational modification] 358220014466 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220014467 ATP binding site [chemical binding]; other site 358220014468 Mg2+ binding site [ion binding]; other site 358220014469 G-X-G motif; other site 358220014470 Predicted amidohydrolase [General function prediction only]; Region: COG0388 358220014471 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 358220014472 putative active site [active] 358220014473 catalytic triad [active] 358220014474 dimer interface [polypeptide binding]; other site 358220014475 TIGR02099 family protein; Region: TIGR02099 358220014476 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 358220014477 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 358220014478 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 358220014479 metal binding triad; other site 358220014480 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 358220014481 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 358220014482 metal binding triad; other site 358220014483 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220014484 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 358220014485 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 358220014486 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 358220014487 HlyD family secretion protein; Region: HlyD_3; pfam13437 358220014488 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 358220014489 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 358220014490 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 358220014491 catalytic residues [active] 358220014492 dimer interface [polypeptide binding]; other site 358220014493 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 358220014494 hydroxyglutarate oxidase; Provisional; Region: PRK11728 358220014495 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 358220014496 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 358220014497 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 358220014498 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220014499 S-adenosylmethionine binding site [chemical binding]; other site 358220014500 MFS/sugar transport protein; Region: MFS_2; pfam13347 358220014501 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 358220014502 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 358220014503 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220014504 short chain dehydrogenase; Provisional; Region: PRK06101 358220014505 NAD(P) binding site [chemical binding]; other site 358220014506 active site 358220014507 SnoaL-like domain; Region: SnoaL_2; pfam12680 358220014508 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 358220014509 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 358220014510 dimer interface [polypeptide binding]; other site 358220014511 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 358220014512 shikimate 5-dehydrogenase; Reviewed; Region: PRK12549 358220014513 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 358220014514 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 358220014515 shikimate binding site; other site 358220014516 NAD(P) binding site [chemical binding]; other site 358220014517 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 358220014518 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 358220014519 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 358220014520 DctM-like transporters; Region: DctM; pfam06808 358220014521 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 358220014522 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 358220014523 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 358220014524 putative glutathione S-transferase; Provisional; Region: PRK10357 358220014525 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 358220014526 putative C-terminal domain interface [polypeptide binding]; other site 358220014527 putative GSH binding site (G-site) [chemical binding]; other site 358220014528 putative dimer interface [polypeptide binding]; other site 358220014529 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 358220014530 dimer interface [polypeptide binding]; other site 358220014531 N-terminal domain interface [polypeptide binding]; other site 358220014532 putative substrate binding pocket (H-site) [chemical binding]; other site 358220014533 adenylosuccinate lyase; Provisional; Region: PRK09285 358220014534 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 358220014535 tetramer interface [polypeptide binding]; other site 358220014536 YaeQ protein; Region: YaeQ; pfam07152 358220014537 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 358220014538 Protein of unknown function (DUF3717); Region: DUF3717; pfam12512 358220014539 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 358220014540 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 358220014541 Predicted membrane protein [Function unknown]; Region: COG1950 358220014542 Peptidase family M48; Region: Peptidase_M48; cl12018 358220014543 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 358220014544 trimer interface [polypeptide binding]; other site 358220014545 dimer interface [polypeptide binding]; other site 358220014546 putative active site [active] 358220014547 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 358220014548 O-Antigen ligase; Region: Wzy_C; pfam04932 358220014549 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 358220014550 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 358220014551 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 358220014552 Pilin (bacterial filament); Region: Pilin; pfam00114 358220014553 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 358220014554 CHASE2 domain; Region: CHASE2; pfam05226 358220014555 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 358220014556 cyclase homology domain; Region: CHD; cd07302 358220014557 nucleotidyl binding site; other site 358220014558 metal binding site [ion binding]; metal-binding site 358220014559 dimer interface [polypeptide binding]; other site 358220014560 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 358220014561 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 358220014562 phosphopeptide binding site; other site 358220014563 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 358220014564 active site 358220014565 CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria; Region: CHASE2; smart01080 358220014566 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 358220014567 Catalytic domain of Protein Kinases; Region: PKc; cd00180 358220014568 active site 358220014569 ATP binding site [chemical binding]; other site 358220014570 substrate binding site [chemical binding]; other site 358220014571 activation loop (A-loop); other site 358220014572 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 358220014573 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 358220014574 CoA binding domain; Region: CoA_binding; smart00881 358220014575 CoA-ligase; Region: Ligase_CoA; pfam00549 358220014576 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 358220014577 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 358220014578 CoA-ligase; Region: Ligase_CoA; pfam00549 358220014579 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 358220014580 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 358220014581 recombination regulator RecX; Reviewed; Region: recX; PRK00117 358220014582 RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange; Region: recA; cd00983 358220014583 hexamer interface [polypeptide binding]; other site 358220014584 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 358220014585 Walker A motif; other site 358220014586 ATP binding site [chemical binding]; other site 358220014587 Walker B motif; other site 358220014588 Transcriptional regulators [Transcription]; Region: MarR; COG1846 358220014589 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 358220014590 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014591 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220014592 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220014593 dimerization interface [polypeptide binding]; other site 358220014594 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220014595 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 358220014596 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 358220014597 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 358220014598 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220014599 active site 358220014600 phosphorylation site [posttranslational modification] 358220014601 intermolecular recognition site; other site 358220014602 dimerization interface [polypeptide binding]; other site 358220014603 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 358220014604 DNA binding site [nucleotide binding] 358220014605 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 358220014606 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220014607 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220014608 dimer interface [polypeptide binding]; other site 358220014609 phosphorylation site [posttranslational modification] 358220014610 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220014611 ATP binding site [chemical binding]; other site 358220014612 Mg2+ binding site [ion binding]; other site 358220014613 G-X-G motif; other site 358220014614 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 358220014615 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 358220014616 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 358220014617 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 358220014618 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 358220014619 SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Region: SET; smart00317 358220014620 Proteins containing SET domain [General function prediction only]; Region: COG2940 358220014621 DNA topoisomerase III; Validated; Region: PRK08173 358220014622 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 358220014623 active site 358220014624 putative interdomain interaction site [polypeptide binding]; other site 358220014625 putative metal-binding site [ion binding]; other site 358220014626 putative nucleotide binding site [chemical binding]; other site 358220014627 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 358220014628 domain I; other site 358220014629 DNA binding groove [nucleotide binding] 358220014630 phosphate binding site [ion binding]; other site 358220014631 domain II; other site 358220014632 domain III; other site 358220014633 nucleotide binding site [chemical binding]; other site 358220014634 catalytic site [active] 358220014635 domain IV; other site 358220014636 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 358220014637 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 358220014638 SWI complex, BAF60b domains; Region: SWIB; smart00151 358220014639 Protein of unknown function (DUF2834); Region: DUF2834; pfam11196 358220014640 Helix-turn-helix domain; Region: HTH_18; pfam12833 358220014641 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 358220014642 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 358220014643 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 358220014644 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220014645 putative substrate translocation pore; other site 358220014646 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220014647 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220014648 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 358220014649 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 358220014650 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 358220014651 Methyltransferase domain; Region: Methyltransf_23; pfam13489 358220014652 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220014653 S-adenosylmethionine binding site [chemical binding]; other site 358220014654 Uncharacterized conserved protein [Function unknown]; Region: COG3148 358220014655 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 358220014656 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220014657 Coenzyme A binding pocket [chemical binding]; other site 358220014658 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 358220014659 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 358220014660 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 358220014661 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 358220014662 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220014663 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220014664 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 358220014665 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 358220014666 dimer interface [polypeptide binding]; other site 358220014667 ssDNA binding site [nucleotide binding]; other site 358220014668 tetramer (dimer of dimers) interface [polypeptide binding]; other site 358220014669 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 358220014670 Inhibitor of apoptosis-promoting Bax1; Region: Bax1-I; pfam01027 358220014671 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 358220014672 tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs; Region: tRNA_Me_trans; cd01998 358220014673 Ligand Binding Site [chemical binding]; other site 358220014674 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220014675 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014676 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 358220014677 putative dimerization interface [polypeptide binding]; other site 358220014678 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2828 358220014679 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220014680 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 358220014681 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 358220014682 trimer interface [polypeptide binding]; other site 358220014683 eyelet of channel; other site 358220014684 L-lactate permease; Region: Lactate_perm; cl00701 358220014685 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 358220014686 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 358220014687 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014688 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 358220014689 putative dimerization interface [polypeptide binding]; other site 358220014690 tricarballylate dehydrogenase; Validated; Region: PRK08274 358220014691 tricarballylate utilization protein B; Provisional; Region: PRK15033 358220014692 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220014693 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 358220014694 nudix motif; other site 358220014695 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220014696 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014697 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 358220014698 substrate binding pocket [chemical binding]; other site 358220014699 dimerization interface [polypeptide binding]; other site 358220014700 benzoylformate decarboxylase; Reviewed; Region: PRK07092 358220014701 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 358220014702 PYR/PP interface [polypeptide binding]; other site 358220014703 dimer interface [polypeptide binding]; other site 358220014704 TPP binding site [chemical binding]; other site 358220014705 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 358220014706 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 358220014707 TPP-binding site [chemical binding]; other site 358220014708 dimer interface [polypeptide binding]; other site 358220014709 Salicylaldehyde dehydrogenase, DoxF-like; Region: ALDH_SaliADH; cd07105 358220014710 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 358220014711 NAD(P) binding site [chemical binding]; other site 358220014712 catalytic residues [active] 358220014713 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 358220014714 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 358220014715 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 358220014716 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 358220014717 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 358220014718 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 358220014719 phosphate binding site [ion binding]; other site 358220014720 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 358220014721 Coenzyme A binding pocket [chemical binding]; other site 358220014722 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 358220014723 Lumazine binding domain; Region: Lum_binding; pfam00677 358220014724 Lumazine binding domain; Region: Lum_binding; pfam00677 358220014725 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4222 358220014726 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 358220014727 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220014728 active site 358220014729 phosphorylation site [posttranslational modification] 358220014730 intermolecular recognition site; other site 358220014731 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 358220014732 Zn2+ binding site [ion binding]; other site 358220014733 Mg2+ binding site [ion binding]; other site 358220014734 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 358220014735 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 358220014736 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 358220014737 PAS domain S-box; Region: sensory_box; TIGR00229 358220014738 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220014739 putative active site [active] 358220014740 heme pocket [chemical binding]; other site 358220014741 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220014742 PAS fold; Region: PAS_3; pfam08447 358220014743 putative active site [active] 358220014744 heme pocket [chemical binding]; other site 358220014745 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220014746 PAS domain; Region: PAS_9; pfam13426 358220014747 putative active site [active] 358220014748 heme pocket [chemical binding]; other site 358220014749 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 358220014750 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 358220014751 dimer interface [polypeptide binding]; other site 358220014752 phosphorylation site [posttranslational modification] 358220014753 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 358220014754 ATP binding site [chemical binding]; other site 358220014755 G-X-G motif; other site 358220014756 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 358220014757 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220014758 active site 358220014759 phosphorylation site [posttranslational modification] 358220014760 intermolecular recognition site; other site 358220014761 dimerization interface [polypeptide binding]; other site 358220014762 spermidine synthase; Provisional; Region: PRK03612 358220014763 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220014764 S-adenosylmethionine binding site [chemical binding]; other site 358220014765 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 358220014766 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 358220014767 Transcription elongation factor Elf1 like; Region: Elf1; cl02038 358220014768 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 358220014769 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 358220014770 Short C-terminal domain; Region: SHOCT; pfam09851 358220014771 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 358220014772 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 358220014773 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 358220014774 Transcriptional regulator [Transcription]; Region: LysR; COG0583 358220014775 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014776 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 358220014777 dimerization interface [polypeptide binding]; other site 358220014778 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 358220014779 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 358220014780 inhibitor-cofactor binding pocket; inhibition site 358220014781 pyridoxal 5'-phosphate binding site [chemical binding]; other site 358220014782 catalytic residue [active] 358220014783 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 358220014784 Putative amidotransferase; Region: DUF4066; pfam13278 358220014785 conserved cys residue [active] 358220014786 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 358220014787 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 358220014788 tetrameric interface [polypeptide binding]; other site 358220014789 NAD binding site [chemical binding]; other site 358220014790 catalytic residues [active] 358220014791 Malate dehydrogenase enzyme; Region: Malate_DH; pfam12434 358220014792 malic enzyme; Reviewed; Region: PRK12862 358220014793 Malic enzyme, N-terminal domain; Region: malic; pfam00390 358220014794 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 358220014795 putative NAD(P) binding site [chemical binding]; other site 358220014796 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 358220014797 RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate...; Region: RNase_Sa; cd00607 358220014798 active site 358220014799 barstar interaction site; other site 358220014800 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 358220014801 putative RNAase interaction site [polypeptide binding]; other site 358220014802 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 358220014803 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 358220014804 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 358220014805 SurA N-terminal domain; Region: SurA_N; pfam09312 358220014806 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 358220014807 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 358220014808 OstA-like protein; Region: OstA; cl00844 358220014809 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 358220014810 Organic solvent tolerance protein; Region: OstA_C; pfam04453 358220014811 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 358220014812 Phosphotransferase enzyme family; Region: APH; pfam01636 358220014813 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 358220014814 RNA methyltransferase, RsmE family; Region: TIGR00046 358220014815 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220014816 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220014817 metal binding site [ion binding]; metal-binding site 358220014818 active site 358220014819 I-site; other site 358220014820 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 358220014821 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 358220014822 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 358220014823 active site 358220014824 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 358220014825 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 358220014826 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 358220014827 putative ligand binding site [chemical binding]; other site 358220014828 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 358220014829 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 358220014830 dimer interface [polypeptide binding]; other site 358220014831 acyl-activating enzyme (AAE) consensus motif; other site 358220014832 putative active site [active] 358220014833 AMP binding site [chemical binding]; other site 358220014834 putative CoA binding site [chemical binding]; other site 358220014835 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 358220014836 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 358220014837 Flavoprotein; Region: Flavoprotein; pfam02441 358220014838 DGC domain; Region: DGC; pfam08859 358220014839 SCP-2 sterol transfer family; Region: SCP2; cl01225 358220014840 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 358220014841 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 358220014842 putative protease; Provisional; Region: PRK15447 358220014843 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 358220014844 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 358220014845 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 358220014846 Peptidase family U32; Region: Peptidase_U32; pfam01136 358220014847 Major Facilitator Superfamily; Region: MFS_1; pfam07690 358220014848 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 358220014849 putative substrate translocation pore; other site 358220014850 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 358220014851 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 358220014852 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 358220014853 dimerization interface [polypeptide binding]; other site 358220014854 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 358220014855 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 358220014856 putative metal binding site [ion binding]; other site 358220014857 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 358220014858 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 358220014859 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 358220014860 hypothetical protein; Provisional; Region: PRK07907 358220014861 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 358220014862 metal binding site [ion binding]; metal-binding site 358220014863 putative dimer interface [polypeptide binding]; other site 358220014864 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220014865 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220014866 metal binding site [ion binding]; metal-binding site 358220014867 active site 358220014868 I-site; other site 358220014869 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 358220014870 dimerization interface [polypeptide binding]; other site 358220014871 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 358220014872 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 358220014873 dimer interface [polypeptide binding]; other site 358220014874 putative CheW interface [polypeptide binding]; other site 358220014875 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 358220014876 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 358220014877 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 358220014878 putative active site [active] 358220014879 catalytic site [active] 358220014880 putative metal binding site [ion binding]; other site 358220014881 Methyltransferase domain; Region: Methyltransf_23; pfam13489 358220014882 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 358220014883 S-adenosylmethionine binding site [chemical binding]; other site 358220014884 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 358220014885 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 358220014886 Predicted membrane protein [Function unknown]; Region: COG2119 358220014887 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 358220014888 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 358220014889 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 358220014890 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 358220014891 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 358220014892 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 358220014893 short chain dehydrogenase; Provisional; Region: PRK07024 358220014894 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 358220014895 NAD(P) binding site [chemical binding]; other site 358220014896 active site 358220014897 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 358220014898 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 358220014899 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 358220014900 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 358220014901 active site 358220014902 motif I; other site 358220014903 motif II; other site 358220014904 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 358220014905 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 358220014906 putative active site [active] 358220014907 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 358220014908 putative cation:proton antiport protein; Provisional; Region: PRK10669 358220014909 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 358220014910 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 358220014911 TrkA-N domain; Region: TrkA_N; pfam02254 358220014912 TrkA-C domain; Region: TrkA_C; pfam02080 358220014913 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 358220014914 active site 358220014915 phosphorylation site [posttranslational modification] 358220014916 intermolecular recognition site; other site 358220014917 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 358220014918 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 358220014919 PAS fold; Region: PAS_7; pfam12860 358220014920 PAS domain S-box; Region: sensory_box; TIGR00229 358220014921 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 358220014922 putative active site [active] 358220014923 heme pocket [chemical binding]; other site 358220014924 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 358220014925 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 358220014926 metal binding site [ion binding]; metal-binding site 358220014927 active site 358220014928 I-site; other site 358220014929 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 358220014930 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 358220014931 active site 358220014932 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 358220014933 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 358220014934 ligand binding site [chemical binding]; other site 358220014935 flexible hinge region; other site 358220014936 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 358220014937 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 358220014938 trmE is a tRNA modification GTPase; Region: trmE; cd04164 358220014939 G1 box; other site 358220014940 GTP/Mg2+ binding site [chemical binding]; other site 358220014941 Switch I region; other site 358220014942 G2 box; other site 358220014943 Switch II region; other site 358220014944 G3 box; other site 358220014945 G4 box; other site 358220014946 G5 box; other site 358220014947 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 358220014948 putative transposase OrfB; Reviewed; Region: PHA02517 358220014949 Integrase core domain; Region: rve; pfam00665 358220014950 Integrase core domain; Region: rve_3; pfam13683 358220014951 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 358220014952 Homeodomain-like domain; Region: HTH_23; cl17451 358220014953 membrane protein insertase; Provisional; Region: PRK01318 358220014954 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 358220014955 hypothetical protein; Provisional; Region: PRK14389 358220014956 Ribonuclease P; Region: Ribonuclease_P; cl00457 358220014957 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399