-- dump date 20140618_192332 -- class Genbank::misc_feature -- table misc_feature_note -- id note 998088000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 998088000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 998088000003 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 998088000004 Walker A motif; other site 998088000005 ATP binding site [chemical binding]; other site 998088000006 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 998088000007 Walker B motif; other site 998088000008 arginine finger; other site 998088000009 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 998088000010 DnaA box-binding interface [nucleotide binding]; other site 998088000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 998088000012 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 998088000013 putative DNA binding surface [nucleotide binding]; other site 998088000014 dimer interface [polypeptide binding]; other site 998088000015 beta-clamp/clamp loader binding surface; other site 998088000016 beta-clamp/translesion DNA polymerase binding surface; other site 998088000017 recombination protein F; Reviewed; Region: recF; PRK00064 998088000018 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088000019 Walker A/P-loop; other site 998088000020 ATP binding site [chemical binding]; other site 998088000021 Q-loop/lid; other site 998088000022 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088000023 ABC transporter signature motif; other site 998088000024 Walker B; other site 998088000025 D-loop; other site 998088000026 H-loop/switch region; other site 998088000027 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 998088000028 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 998088000029 ATP binding site [chemical binding]; other site 998088000030 Mg2+ binding site [ion binding]; other site 998088000031 G-X-G motif; other site 998088000032 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 998088000033 anchoring element; other site 998088000034 dimer interface [polypeptide binding]; other site 998088000035 ATP binding site [chemical binding]; other site 998088000036 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 998088000037 active site 998088000038 putative metal-binding site [ion binding]; other site 998088000039 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 998088000040 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 998088000041 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 998088000042 conserved cys residue [active] 998088000043 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088000044 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088000045 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 998088000046 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 998088000047 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 998088000048 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 998088000049 putative dimer interface [polypeptide binding]; other site 998088000050 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 998088000051 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 998088000052 putative dimer interface [polypeptide binding]; other site 998088000053 valine--pyruvate transaminase; Provisional; Region: avtA; PRK09440 998088000054 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 998088000055 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088000056 homodimer interface [polypeptide binding]; other site 998088000057 catalytic residue [active] 998088000058 Helix-turn-helix domain; Region: HTH_18; pfam12833 998088000059 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 998088000060 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 998088000061 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 998088000062 active site 998088000063 phosphorylation site [posttranslational modification] 998088000064 intermolecular recognition site; other site 998088000065 dimerization interface [polypeptide binding]; other site 998088000066 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 998088000067 DNA binding site [nucleotide binding] 998088000068 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 998088000069 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 998088000070 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 998088000071 Ligand Binding Site [chemical binding]; other site 998088000072 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 998088000073 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 998088000074 dimer interface [polypeptide binding]; other site 998088000075 phosphorylation site [posttranslational modification] 998088000076 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 998088000077 ATP binding site [chemical binding]; other site 998088000078 Mg2+ binding site [ion binding]; other site 998088000079 G-X-G motif; other site 998088000080 K+-transporting ATPase, c chain; Region: KdpC; cl00944 998088000081 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 998088000082 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 998088000083 Soluble P-type ATPase [General function prediction only]; Region: COG4087 998088000084 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 998088000085 glutathione reductase; Validated; Region: PRK06116 998088000086 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088000087 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088000088 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088000089 HAMP domain; Region: HAMP; pfam00672 998088000090 PAS domain; Region: PAS_9; pfam13426 998088000091 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 998088000092 putative active site [active] 998088000093 heme pocket [chemical binding]; other site 998088000094 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088000095 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 998088000096 ATP binding site [chemical binding]; other site 998088000097 Mg2+ binding site [ion binding]; other site 998088000098 G-X-G motif; other site 998088000099 multidrug efflux protein; Reviewed; Region: PRK09579 998088000100 Protein export membrane protein; Region: SecD_SecF; cl14618 998088000101 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088000102 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 998088000103 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088000104 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088000105 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088000106 Ricin-type beta-trefoil; Region: RICIN; smart00458 998088000107 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 998088000108 putative sugar binding sites [chemical binding]; other site 998088000109 Q-X-W motif; other site 998088000110 putative hydrolase; Provisional; Region: PRK10976 998088000111 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 998088000112 active site 998088000113 motif I; other site 998088000114 motif II; other site 998088000115 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 998088000116 lysophospholipase L2; Provisional; Region: PRK10749 998088000117 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 998088000118 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 998088000119 trimer interface [polypeptide binding]; other site 998088000120 active site 998088000121 CoA binding site [chemical binding]; other site 998088000122 tRNA guanosine-2'-O-methyltransferase; Provisional; Region: PRK11081 998088000123 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 998088000124 SpoU, rRNA methylase, C-terminal; Region: SpoU_methylas_C; pfam12105 998088000125 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 998088000126 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088000127 Zn2+ binding site [ion binding]; other site 998088000128 Mg2+ binding site [ion binding]; other site 998088000129 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 998088000130 synthetase active site [active] 998088000131 NTP binding site [chemical binding]; other site 998088000132 metal binding site [ion binding]; metal-binding site 998088000133 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 998088000134 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 998088000135 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 998088000136 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 998088000137 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 998088000138 catalytic site [active] 998088000139 G-X2-G-X-G-K; other site 998088000140 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 998088000141 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 998088000142 putative active site [active] 998088000143 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 998088000144 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; pfam06293 998088000145 PAS fold; Region: PAS_3; pfam08447 998088000146 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088000147 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000148 metal binding site [ion binding]; metal-binding site 998088000149 active site 998088000150 I-site; other site 998088000151 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 998088000152 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 998088000153 EamA-like transporter family; Region: EamA; pfam00892 998088000154 EamA-like transporter family; Region: EamA; pfam00892 998088000155 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088000156 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088000157 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 998088000158 substrate binding pocket [chemical binding]; other site 998088000159 dimerization interface [polypeptide binding]; other site 998088000160 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 998088000161 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 998088000162 active site 998088000163 HIGH motif; other site 998088000164 dimer interface [polypeptide binding]; other site 998088000165 KMSKS motif; other site 998088000166 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 998088000167 Ligand Binding Site [chemical binding]; other site 998088000168 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 998088000169 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 998088000170 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 998088000171 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 998088000172 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 998088000173 Ferritin-like domain; Region: Ferritin; pfam00210 998088000174 ferroxidase diiron center [ion binding]; other site 998088000175 Predicted flavoproteins [General function prediction only]; Region: COG2081 998088000176 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 998088000177 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 998088000178 GAF domain; Region: GAF_3; pfam13492 998088000179 Histidine kinase; Region: His_kinase; pfam06580 998088000180 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 998088000181 ATP binding site [chemical binding]; other site 998088000182 Mg2+ binding site [ion binding]; other site 998088000183 G-X-G motif; other site 998088000184 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 998088000185 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 998088000186 active site 998088000187 phosphorylation site [posttranslational modification] 998088000188 intermolecular recognition site; other site 998088000189 dimerization interface [polypeptide binding]; other site 998088000190 LytTr DNA-binding domain; Region: LytTR; pfam04397 998088000191 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 998088000192 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 998088000193 putative substrate translocation pore; other site 998088000194 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 998088000195 XdhC Rossmann domain; Region: XdhC_C; pfam13478 998088000196 ATP-grasp domain; Region: ATP-grasp_4; cl17255 998088000197 AIR carboxylase; Region: AIRC; pfam00731 998088000198 Domain of unknown function (DUF897); Region: DUF897; cl01312 998088000199 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 998088000200 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088000201 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 998088000202 dimerization interface [polypeptide binding]; other site 998088000203 vitamin B12/cobalamin outer membrane transporter; Provisional; Region: btuB; PRK10641 998088000204 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 998088000205 N-terminal plug; other site 998088000206 ligand-binding site [chemical binding]; other site 998088000207 glutamate racemase; Provisional; Region: PRK00865 998088000208 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 998088000209 RNA recognition motif (RRM) superfamily; Region: RRM_SF; cl17169 998088000210 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 998088000211 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 998088000212 putative ATP binding site [chemical binding]; other site 998088000213 putative substrate interface [chemical binding]; other site 998088000214 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 998088000215 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 998088000216 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 998088000217 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088000218 catalytic residue [active] 998088000219 ATP-dependent DNA helicase Rep; Provisional; Region: PRK10919 998088000220 Part of AAA domain; Region: AAA_19; pfam13245 998088000221 Family description; Region: UvrD_C_2; pfam13538 998088000222 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088000223 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000224 metal binding site [ion binding]; metal-binding site 998088000225 active site 998088000226 I-site; other site 998088000227 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 998088000228 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 998088000229 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 998088000230 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 998088000231 NAD(P) binding site [chemical binding]; other site 998088000232 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 998088000233 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 998088000234 substrate-cofactor binding pocket; other site 998088000235 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088000236 catalytic residue [active] 998088000237 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088000238 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088000239 Bacterial transcriptional repressor; Region: TetR; pfam13972 998088000240 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 998088000241 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 998088000242 NADP binding site [chemical binding]; other site 998088000243 homopentamer interface [polypeptide binding]; other site 998088000244 substrate binding site [chemical binding]; other site 998088000245 active site 998088000246 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 998088000247 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 998088000248 putative ADP-binding pocket [chemical binding]; other site 998088000249 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 998088000250 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 998088000251 putative active site [active] 998088000252 putative metal binding site [ion binding]; other site 998088000253 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 998088000254 O-Antigen ligase; Region: Wzy_C; pfam04932 998088000255 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 998088000256 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 998088000257 Probable Catalytic site; other site 998088000258 metal-binding site 998088000259 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088000260 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 998088000261 substrate binding pocket [chemical binding]; other site 998088000262 membrane-bound complex binding site; other site 998088000263 hinge residues; other site 998088000264 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 998088000265 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088000266 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088000267 LysE type translocator; Region: LysE; cl00565 998088000268 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 998088000269 Protein of unknown function (DUF3313); Region: DUF3313; pfam11769 998088000270 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG3837 998088000271 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 998088000272 YdfZ protein; Region: YdfZ; cl11878 998088000273 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 998088000274 Part of AAA domain; Region: AAA_19; pfam13245 998088000275 Family description; Region: UvrD_C_2; pfam13538 998088000276 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 998088000277 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 998088000278 ligand binding site [chemical binding]; other site 998088000279 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 998088000280 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 998088000281 Walker A/P-loop; other site 998088000282 ATP binding site [chemical binding]; other site 998088000283 Q-loop/lid; other site 998088000284 ABC transporter signature motif; other site 998088000285 Walker B; other site 998088000286 D-loop; other site 998088000287 H-loop/switch region; other site 998088000288 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 998088000289 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 998088000290 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 998088000291 TM-ABC transporter signature motif; other site 998088000292 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 998088000293 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 998088000294 TM-ABC transporter signature motif; other site 998088000295 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 998088000296 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 998088000297 active site 998088000298 metal binding site [ion binding]; metal-binding site 998088000299 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 998088000300 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 998088000301 MgtE intracellular N domain; Region: MgtE_N; smart00924 998088000302 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 998088000303 Divalent cation transporter; Region: MgtE; cl00786 998088000304 siroheme synthase; Provisional; Region: cysG; PRK10637 998088000305 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 998088000306 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 998088000307 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 998088000308 active site 998088000309 SAM binding site [chemical binding]; other site 998088000310 homodimer interface [polypeptide binding]; other site 998088000311 nitrite transporter NirC; Provisional; Region: PRK11562 998088000312 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while...; Region: Rieske_NirD; cd03529 998088000313 nitrite reductase subunit NirD; Provisional; Region: PRK14989 998088000314 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 998088000315 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 998088000316 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 998088000317 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 998088000318 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 998088000319 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 998088000320 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 998088000321 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 998088000322 daunorubicin resistance ABC transporter ATP-binding subunit; Region: drrA; TIGR01188 998088000323 Walker A/P-loop; other site 998088000324 ATP binding site [chemical binding]; other site 998088000325 Q-loop/lid; other site 998088000326 ABC transporter signature motif; other site 998088000327 Walker B; other site 998088000328 D-loop; other site 998088000329 H-loop/switch region; other site 998088000330 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 998088000331 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 998088000332 Walker A/P-loop; other site 998088000333 ATP binding site [chemical binding]; other site 998088000334 Q-loop/lid; other site 998088000335 ABC transporter signature motif; other site 998088000336 Walker B; other site 998088000337 D-loop; other site 998088000338 H-loop/switch region; other site 998088000339 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 998088000340 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088000341 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088000342 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088000343 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088000344 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 998088000345 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 998088000346 Walker A motif; other site 998088000347 ATP binding site [chemical binding]; other site 998088000348 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 998088000349 Walker B motif; other site 998088000350 arginine finger; other site 998088000351 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 998088000352 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 998088000353 active site 998088000354 HslU subunit interaction site [polypeptide binding]; other site 998088000355 cell division protein FtsN; Region: ftsN; TIGR02223 998088000356 Sporulation related domain; Region: SPOR; pfam05036 998088000357 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 998088000358 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 998088000359 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 998088000360 active site 998088000361 HIGH motif; other site 998088000362 KMSK motif region; other site 998088000363 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 998088000364 tRNA binding surface [nucleotide binding]; other site 998088000365 anticodon binding site; other site 998088000366 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 998088000367 RNA polymerase sigma factor; Provisional; Region: PRK11924 998088000368 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088000369 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 998088000370 DNA binding residues [nucleotide binding] 998088000371 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 998088000372 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 998088000373 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 998088000374 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 998088000375 active site 998088000376 catalytic residues [active] 998088000377 galactokinase; Provisional; Region: PRK05101 998088000378 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 998088000379 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 998088000380 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK11720 998088000381 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 998088000382 dimer interface [polypeptide binding]; other site 998088000383 active site 998088000384 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 998088000385 UDP-glucose 4-epimerase; Region: PLN02240 998088000386 NAD binding site [chemical binding]; other site 998088000387 homodimer interface [polypeptide binding]; other site 998088000388 active site 998088000389 substrate binding site [chemical binding]; other site 998088000390 DNA-binding transcriptional regulator GalR; Provisional; Region: PRK10727 998088000391 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088000392 DNA binding site [nucleotide binding] 998088000393 domain linker motif; other site 998088000394 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 998088000395 dimerization interface (closed form) [polypeptide binding]; other site 998088000396 ligand binding site [chemical binding]; other site 998088000397 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 998088000398 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 998088000399 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 998088000400 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 998088000401 Beta galactosidase small chain; Region: Bgal_small_N; pfam02929 998088000402 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional; Region: PRK15395 998088000403 Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Region: PBP1_GGBP; cd01539 998088000404 ligand binding site [chemical binding]; other site 998088000405 calcium binding site [ion binding]; other site 998088000406 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional; Region: PRK10982 998088000407 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 998088000408 Walker A/P-loop; other site 998088000409 ATP binding site [chemical binding]; other site 998088000410 Q-loop/lid; other site 998088000411 ABC transporter signature motif; other site 998088000412 Walker B; other site 998088000413 D-loop; other site 998088000414 H-loop/switch region; other site 998088000415 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 998088000416 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 998088000417 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 998088000418 TM-ABC transporter signature motif; other site 998088000419 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 998088000420 dimerization interface [polypeptide binding]; other site 998088000421 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088000422 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088000423 dimer interface [polypeptide binding]; other site 998088000424 putative CheW interface [polypeptide binding]; other site 998088000425 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 998088000426 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 998088000427 S-adenosylmethionine binding site [chemical binding]; other site 998088000428 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 998088000429 maltodextrin glucosidase; Provisional; Region: PRK10785 998088000430 N-terminal Early set domain associated with the catalytic domain of cyclomaltodextrinase and pullulan-degrading enzymes; Region: E_set_CDase_PDE_N; cd02857 998088000431 homodimer interface [polypeptide binding]; other site 998088000432 Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins; Region: AmyAc_CMD; cd11338 998088000433 active site 998088000434 homodimer interface [polypeptide binding]; other site 998088000435 catalytic site [active] 998088000436 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 998088000437 HDOD domain; Region: HDOD; pfam08668 998088000438 HD domain; Region: HD; pfam01966 998088000439 META domain; Region: META; cl01245 998088000440 putative chaperone; Provisional; Region: PRK11678 998088000441 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 998088000442 nucleotide binding site [chemical binding]; other site 998088000443 putative NEF/HSP70 interaction site [polypeptide binding]; other site 998088000444 SBD interface [polypeptide binding]; other site 998088000445 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 998088000446 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 998088000447 putative ligand binding site [chemical binding]; other site 998088000448 putative NAD binding site [chemical binding]; other site 998088000449 catalytic site [active] 998088000450 CreA protein; Region: CreA; pfam05981 998088000451 Protein of unknown function (DUF962); Region: DUF962; cl01879 998088000452 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 998088000453 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 998088000454 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 998088000455 putative aminotransferase; Validated; Region: PRK07480 998088000456 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 998088000457 inhibitor-cofactor binding pocket; inhibition site 998088000458 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088000459 catalytic residue [active] 998088000460 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 998088000461 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 998088000462 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 998088000463 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 998088000464 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 998088000465 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088000466 Walker A/P-loop; other site 998088000467 ATP binding site [chemical binding]; other site 998088000468 Q-loop/lid; other site 998088000469 ABC transporter signature motif; other site 998088000470 Walker B; other site 998088000471 D-loop; other site 998088000472 H-loop/switch region; other site 998088000473 TOBE domain; Region: TOBE_2; pfam08402 998088000474 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 998088000475 dimer interface [polypeptide binding]; other site 998088000476 conserved gate region; other site 998088000477 putative PBP binding loops; other site 998088000478 ABC-ATPase subunit interface; other site 998088000479 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 998088000480 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 998088000481 dimer interface [polypeptide binding]; other site 998088000482 conserved gate region; other site 998088000483 putative PBP binding loops; other site 998088000484 ABC-ATPase subunit interface; other site 998088000485 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 998088000486 MOSC domain; Region: MOSC; pfam03473 998088000487 3-alpha domain; Region: 3-alpha; pfam03475 998088000488 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 998088000489 CoenzymeA binding site [chemical binding]; other site 998088000490 subunit interaction site [polypeptide binding]; other site 998088000491 PHB binding site; other site 998088000492 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 998088000493 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 998088000494 ATP binding site [chemical binding]; other site 998088000495 putative Mg++ binding site [ion binding]; other site 998088000496 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 998088000497 nucleotide binding region [chemical binding]; other site 998088000498 ATP-binding site [chemical binding]; other site 998088000499 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 998088000500 HRDC domain; Region: HRDC; pfam00570 998088000501 Cytochrome c; Region: Cytochrom_C; cl11414 998088000502 Uncharacterized conserved protein [Function unknown]; Region: COG0397 998088000503 hypothetical protein; Validated; Region: PRK00029 998088000504 Protein of unknown function (DUF3630); Region: DUF3630; pfam12305 998088000505 hypothetical protein; Provisional; Region: PRK11212 998088000506 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 998088000507 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088000508 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088000509 dimer interface [polypeptide binding]; other site 998088000510 putative CheW interface [polypeptide binding]; other site 998088000511 CpeT/CpcT family (DUF1001); Region: CpeT; pfam06206 998088000512 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 998088000513 primosome assembly protein PriA; Validated; Region: PRK05580 998088000514 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 998088000515 ATP binding site [chemical binding]; other site 998088000516 putative Mg++ binding site [ion binding]; other site 998088000517 helicase superfamily c-terminal domain; Region: HELICc; smart00490 998088000518 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088000519 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 998088000520 NAD(P) binding site [chemical binding]; other site 998088000521 active site 998088000522 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 998088000523 aromatic amino acid transport protein; Region: araaP; TIGR00837 998088000524 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 998088000525 Malic enzyme, N-terminal domain; Region: malic; pfam00390 998088000526 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 998088000527 putative NAD(P) binding site [chemical binding]; other site 998088000528 hypothetical protein; Reviewed; Region: PRK01637 998088000529 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 998088000530 putative active site [active] 998088000531 dimerization interface [polypeptide binding]; other site 998088000532 putative tRNAtyr binding site [nucleotide binding]; other site 998088000533 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 998088000534 S-adenosylmethionine binding site [chemical binding]; other site 998088000535 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 998088000536 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088000537 Coenzyme A binding pocket [chemical binding]; other site 998088000538 Putative thioesterase (yiiD_Cterm); Region: YiiD_Cterm; pfam09500 998088000539 AsmA family; Region: AsmA; pfam05170 998088000540 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 998088000541 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 998088000542 Y-family of DNA polymerases; Region: PolY; cl12025 998088000543 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 998088000544 ssDNA binding site; other site 998088000545 generic binding surface II; other site 998088000546 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 998088000547 ATP binding site [chemical binding]; other site 998088000548 putative Mg++ binding site [ion binding]; other site 998088000549 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 998088000550 nucleotide binding region [chemical binding]; other site 998088000551 ATP-binding site [chemical binding]; other site 998088000552 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 998088000553 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 998088000554 domain interface [polypeptide binding]; other site 998088000555 putative active site [active] 998088000556 catalytic site [active] 998088000557 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 998088000558 domain interface [polypeptide binding]; other site 998088000559 putative active site [active] 998088000560 catalytic site [active] 998088000561 low affinity gluconate transporter; Provisional; Region: PRK10472 998088000562 GntP family permease; Region: GntP_permease; pfam02447 998088000563 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 998088000564 ATP-binding site [chemical binding]; other site 998088000565 Gluconate-6-phosphate binding site [chemical binding]; other site 998088000566 Shikimate kinase; Region: SKI; pfam01202 998088000567 phosphogluconate dehydratase; Validated; Region: PRK09054 998088000568 6-phosphogluconate dehydratase; Region: edd; TIGR01196 998088000569 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 998088000570 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 998088000571 active site 998088000572 intersubunit interface [polypeptide binding]; other site 998088000573 catalytic residue [active] 998088000574 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 998088000575 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088000576 DNA binding site [nucleotide binding] 998088000577 domain linker motif; other site 998088000578 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 998088000579 putative ligand binding site [chemical binding]; other site 998088000580 putative dimerization interface [polypeptide binding]; other site 998088000581 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 998088000582 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 998088000583 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 998088000584 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 998088000585 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 998088000586 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 998088000587 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088000588 phosphoglyceromutase; Provisional; Region: PRK05434 998088000589 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 998088000590 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 998088000591 active site residue [active] 998088000592 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 998088000593 SecA binding site; other site 998088000594 Preprotein binding site; other site 998088000595 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 998088000596 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 998088000597 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 998088000598 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 998088000599 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 998088000600 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 998088000601 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 998088000602 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 998088000603 active site 998088000604 carboxylesterase BioH; Provisional; Region: PRK10349 998088000605 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 998088000606 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 998088000607 SprA-related family; Region: SprA-related; pfam12118 998088000608 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 998088000609 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 998088000610 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 998088000611 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 998088000612 RNA binding site [nucleotide binding]; other site 998088000613 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 998088000614 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 998088000615 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 998088000616 osmolarity response regulator; Provisional; Region: ompR; PRK09468 998088000617 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 998088000618 active site 998088000619 phosphorylation site [posttranslational modification] 998088000620 intermolecular recognition site; other site 998088000621 dimerization interface [polypeptide binding]; other site 998088000622 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 998088000623 DNA binding site [nucleotide binding] 998088000624 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 998088000625 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 998088000626 dimerization interface [polypeptide binding]; other site 998088000627 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 998088000628 dimer interface [polypeptide binding]; other site 998088000629 phosphorylation site [posttranslational modification] 998088000630 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 998088000631 ATP binding site [chemical binding]; other site 998088000632 Mg2+ binding site [ion binding]; other site 998088000633 G-X-G motif; other site 998088000634 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088000635 EamA-like transporter family; Region: EamA; pfam00892 998088000636 EamA-like transporter family; Region: EamA; pfam00892 998088000637 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 998088000638 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 998088000639 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 998088000640 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 998088000641 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 998088000642 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 998088000643 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 998088000644 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 998088000645 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 998088000646 putative translocon binding site; other site 998088000647 protein-rRNA interface [nucleotide binding]; other site 998088000648 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 998088000649 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 998088000650 G-X-X-G motif; other site 998088000651 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 998088000652 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 998088000653 23S rRNA interface [nucleotide binding]; other site 998088000654 5S rRNA interface [nucleotide binding]; other site 998088000655 putative antibiotic binding site [chemical binding]; other site 998088000656 L25 interface [polypeptide binding]; other site 998088000657 L27 interface [polypeptide binding]; other site 998088000658 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 998088000659 23S rRNA interface [nucleotide binding]; other site 998088000660 putative translocon interaction site; other site 998088000661 signal recognition particle (SRP54) interaction site; other site 998088000662 L23 interface [polypeptide binding]; other site 998088000663 trigger factor interaction site; other site 998088000664 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 998088000665 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 998088000666 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 998088000667 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 998088000668 RNA binding site [nucleotide binding]; other site 998088000669 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 998088000670 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 998088000671 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 998088000672 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 998088000673 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 998088000674 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 998088000675 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 998088000676 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 998088000677 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 998088000678 5S rRNA interface [nucleotide binding]; other site 998088000679 23S rRNA interface [nucleotide binding]; other site 998088000680 L5 interface [polypeptide binding]; other site 998088000681 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 998088000682 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 998088000683 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 998088000684 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 998088000685 23S rRNA binding site [nucleotide binding]; other site 998088000686 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 998088000687 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 998088000688 SecY translocase; Region: SecY; pfam00344 998088000689 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 998088000690 30S ribosomal protein S13; Region: bact_S13; TIGR03631 998088000691 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 998088000692 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 998088000693 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 998088000694 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 998088000695 RNA binding surface [nucleotide binding]; other site 998088000696 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 998088000697 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 998088000698 alphaNTD homodimer interface [polypeptide binding]; other site 998088000699 alphaNTD - beta interaction site [polypeptide binding]; other site 998088000700 alphaNTD - beta' interaction site [polypeptide binding]; other site 998088000701 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 998088000702 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 998088000703 putative outer membrane receptor; Provisional; Region: PRK13513 998088000704 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 998088000705 N-terminal plug; other site 998088000706 ligand-binding site [chemical binding]; other site 998088000707 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088000708 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 998088000709 substrate binding pocket [chemical binding]; other site 998088000710 membrane-bound complex binding site; other site 998088000711 hinge residues; other site 998088000712 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088000713 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000714 metal binding site [ion binding]; metal-binding site 998088000715 active site 998088000716 I-site; other site 998088000717 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088000718 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 998088000719 dimerization interface [polypeptide binding]; other site 998088000720 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 998088000721 dimer interface [polypeptide binding]; other site 998088000722 phosphorylation site [posttranslational modification] 998088000723 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 998088000724 ATP binding site [chemical binding]; other site 998088000725 Mg2+ binding site [ion binding]; other site 998088000726 G-X-G motif; other site 998088000727 osmolarity response regulator; Provisional; Region: ompR; PRK09468 998088000728 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 998088000729 active site 998088000730 phosphorylation site [posttranslational modification] 998088000731 intermolecular recognition site; other site 998088000732 dimerization interface [polypeptide binding]; other site 998088000733 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 998088000734 DNA binding site [nucleotide binding] 998088000735 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088000736 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 998088000737 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 998088000738 dimerization interface [polypeptide binding]; other site 998088000739 Pirin-related protein [General function prediction only]; Region: COG1741 998088000740 Pirin; Region: Pirin; pfam02678 998088000741 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 998088000742 Predicted membrane protein [Function unknown]; Region: COG2259 998088000743 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 998088000744 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 998088000745 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 998088000746 Family description; Region: UvrD_C_2; pfam13538 998088000747 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 998088000748 AAA domain; Region: AAA_30; pfam13604 998088000749 Family description; Region: UvrD_C_2; pfam13538 998088000750 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 998088000751 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088000752 Coenzyme A binding pocket [chemical binding]; other site 998088000753 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 998088000754 PAS fold; Region: PAS_3; pfam08447 998088000755 putative active site [active] 998088000756 heme pocket [chemical binding]; other site 998088000757 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088000758 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000759 metal binding site [ion binding]; metal-binding site 998088000760 active site 998088000761 I-site; other site 998088000762 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 998088000763 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 998088000764 non-specific DNA binding site [nucleotide binding]; other site 998088000765 salt bridge; other site 998088000766 sequence-specific DNA binding site [nucleotide binding]; other site 998088000767 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088000768 transcriptional regulator protein; Region: phnR; TIGR03337 998088000769 DNA-binding site [nucleotide binding]; DNA binding site 998088000770 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 998088000771 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 998088000772 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 998088000773 Uncharacterized proteins of the AP superfamily [General function prediction only]; Region: COG1524 998088000774 Sulfatase; Region: Sulfatase; cl17466 998088000775 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 998088000776 dimer interface [polypeptide binding]; other site 998088000777 conserved gate region; other site 998088000778 ABC-ATPase subunit interface; other site 998088000779 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 998088000780 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 998088000781 dimer interface [polypeptide binding]; other site 998088000782 conserved gate region; other site 998088000783 putative PBP binding loops; other site 998088000784 ABC-ATPase subunit interface; other site 998088000785 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 998088000786 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088000787 Walker A/P-loop; other site 998088000788 ATP binding site [chemical binding]; other site 998088000789 Q-loop/lid; other site 998088000790 ABC transporter signature motif; other site 998088000791 Walker B; other site 998088000792 D-loop; other site 998088000793 H-loop/switch region; other site 998088000794 TOBE domain; Region: TOBE_2; pfam08402 998088000795 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 998088000796 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 998088000797 Cache domain; Region: Cache_1; pfam02743 998088000798 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088000799 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088000800 metal binding site [ion binding]; metal-binding site 998088000801 active site 998088000802 I-site; other site 998088000803 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 998088000804 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088000805 EamA-like transporter family; Region: EamA; pfam00892 998088000806 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 998088000807 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 998088000808 putative C-terminal domain interface [polypeptide binding]; other site 998088000809 putative GSH binding site (G-site) [chemical binding]; other site 998088000810 putative dimer interface [polypeptide binding]; other site 998088000811 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 998088000812 N-terminal domain interface [polypeptide binding]; other site 998088000813 dimer interface [polypeptide binding]; other site 998088000814 substrate binding pocket (H-site) [chemical binding]; other site 998088000815 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 998088000816 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 998088000817 homodimer interface [polypeptide binding]; other site 998088000818 substrate-cofactor binding pocket; other site 998088000819 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088000820 catalytic residue [active] 998088000821 transcriptional regulator SgrR; Provisional; Region: PRK13626 998088000822 Sugar transport-related sRNA regulator N-term; Region: SgrR_N; pfam12793 998088000823 The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold; Region: PBP2_SgrR_like; cd08507 998088000824 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 998088000825 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 998088000826 dimer interface [polypeptide binding]; other site 998088000827 active site 998088000828 heme binding site [chemical binding]; other site 998088000829 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 998088000830 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 998088000831 active site 998088000832 Protein of unknown function (DUF2288); Region: DUF2288; cl02399 998088000833 Proteobacterial lipase chaperone protein; Region: Lipase_chap; pfam03280 998088000834 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 998088000835 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 998088000836 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 998088000837 active site 998088000838 HIGH motif; other site 998088000839 dimer interface [polypeptide binding]; other site 998088000840 KMSKS motif; other site 998088000841 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 998088000842 RNA binding surface [nucleotide binding]; other site 998088000843 Transcriptional regulator of RNA polII, SAGA, subunit; Region: SAGA-Tad1; pfam12767 998088000844 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 998088000845 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 998088000846 DNA binding residues [nucleotide binding] 998088000847 dimerization interface [polypeptide binding]; other site 998088000848 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 998088000849 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088000850 substrate binding pocket [chemical binding]; other site 998088000851 membrane-bound complex binding site; other site 998088000852 hinge residues; other site 998088000853 Protein of unknown function (DUF1496); Region: DUF1496; pfam07383 998088000854 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 998088000855 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 998088000856 tetramer interface [polypeptide binding]; other site 998088000857 heme binding pocket [chemical binding]; other site 998088000858 NADPH binding site [chemical binding]; other site 998088000859 putative acetyltransferase YhhY; Provisional; Region: PRK10140 998088000860 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 998088000861 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088000862 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088000863 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 998088000864 Superinfection exclusion protein B; Region: SieB; pfam14163 998088000865 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 998088000866 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 998088000867 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 998088000868 HIGH motif; other site 998088000869 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 998088000870 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 998088000871 active site 998088000872 KMSKS motif; other site 998088000873 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 998088000874 tRNA binding surface [nucleotide binding]; other site 998088000875 anticodon binding site; other site 998088000876 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 998088000877 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 998088000878 multifunctional aminopeptidase A; Provisional; Region: PRK00913 998088000879 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 998088000880 interface (dimer of trimers) [polypeptide binding]; other site 998088000881 Substrate-binding/catalytic site; other site 998088000882 Zn-binding sites [ion binding]; other site 998088000883 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 998088000884 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 998088000885 lipopolysaccharide ABC transporter permease; Provisional; Region: PRK15071 998088000886 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 998088000887 RDD family; Region: RDD; pfam06271 998088000888 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 998088000889 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 998088000890 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 998088000891 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 998088000892 N-terminal plug; other site 998088000893 ligand-binding site [chemical binding]; other site 998088000894 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 998088000895 Acyltransferase family; Region: Acyl_transf_3; pfam01757 998088000896 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 998088000897 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 998088000898 inner membrane transporter YjeM; Provisional; Region: PRK15238 998088000899 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 998088000900 EamA-like transporter family; Region: EamA; pfam00892 998088000901 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 998088000902 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 998088000903 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 998088000904 trimer interface [polypeptide binding]; other site 998088000905 eyelet of channel; other site 998088000906 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 998088000907 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 998088000908 putative active site [active] 998088000909 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 998088000910 HemY protein N-terminus; Region: HemY_N; pfam07219 998088000911 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 998088000912 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 998088000913 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 998088000914 active site 998088000915 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 998088000916 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 998088000917 domain interfaces; other site 998088000918 active site 998088000919 adenylate cyclase; Provisional; Region: cyaA; PRK09450 998088000920 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 998088000921 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 998088000922 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 998088000923 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate...; Region: Frataxin; cd00503 998088000924 putative iron binding site [ion binding]; other site 998088000925 diaminopimelate decarboxylase; Region: lysA; TIGR01048 998088000926 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 998088000927 active site 998088000928 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088000929 substrate binding site [chemical binding]; other site 998088000930 catalytic residues [active] 998088000931 dimer interface [polypeptide binding]; other site 998088000932 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 998088000933 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 998088000934 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 998088000935 Protein of unknown function, DUF484; Region: DUF484; cl17449 998088000936 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 998088000937 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 998088000938 active site 998088000939 Int/Topo IB signature motif; other site 998088000940 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 998088000941 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 998088000942 motif II; other site 998088000943 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 998088000944 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088000945 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 998088000946 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 998088000947 ligand binding site [chemical binding]; other site 998088000948 flexible hinge region; other site 998088000949 Peptidase C26; Region: Peptidase_C26; pfam07722 998088000950 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 998088000951 catalytic triad [active] 998088000952 hypothetical protein; Provisional; Region: PRK05255 998088000953 peptidase PmbA; Provisional; Region: PRK11040 998088000954 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 998088000955 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 998088000956 hinge; other site 998088000957 active site 998088000958 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 998088000959 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 998088000960 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 998088000961 mce related protein; Region: MCE; pfam02470 998088000962 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 998088000963 conserved hypothetical integral membrane protein; Region: TIGR00056 998088000964 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 998088000965 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 998088000966 Walker A/P-loop; other site 998088000967 ATP binding site [chemical binding]; other site 998088000968 Q-loop/lid; other site 998088000969 ABC transporter signature motif; other site 998088000970 Walker B; other site 998088000971 D-loop; other site 998088000972 H-loop/switch region; other site 998088000973 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 998088000974 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 998088000975 putative active site [active] 998088000976 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 998088000977 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 998088000978 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 998088000979 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 998088000980 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 998088000981 OstA-like protein; Region: OstA; cl00844 998088000982 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 998088000983 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 998088000984 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 998088000985 Walker A/P-loop; other site 998088000986 ATP binding site [chemical binding]; other site 998088000987 Q-loop/lid; other site 998088000988 ABC transporter signature motif; other site 998088000989 Walker B; other site 998088000990 D-loop; other site 998088000991 H-loop/switch region; other site 998088000992 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 998088000993 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 998088000994 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 998088000995 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 998088000996 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 998088000997 30S subunit binding site; other site 998088000998 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 998088000999 active site 998088001000 phosphorylation site [posttranslational modification] 998088001001 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 998088001002 AAA domain; Region: AAA_18; pfam13238 998088001003 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 998088001004 dimerization domain swap beta strand [polypeptide binding]; other site 998088001005 regulatory protein interface [polypeptide binding]; other site 998088001006 active site 998088001007 regulatory phosphorylation site [posttranslational modification]; other site 998088001008 Transcriptional antiterminator [Transcription]; Region: BglG; COG3711 998088001009 HTH domain; Region: HTH_11; pfam08279 998088001010 Mga helix-turn-helix domain; Region: Mga; pfam05043 998088001011 PRD domain; Region: PRD; pfam00874 998088001012 PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved...; Region: PTS_IIB_bgl_like; cd05568 998088001013 active site 998088001014 P-loop; other site 998088001015 phosphorylation site [posttranslational modification] 998088001016 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 998088001017 active site 998088001018 phosphorylation site [posttranslational modification] 998088001019 conserved hypothetical protein EF_0839/AHA_3917; Region: EF_0839; TIGR03581 998088001020 uncharacterized pyridoxal phosphate-dependent enzyme; Region: selA_rel; TIGR01437 998088001021 probable amidohydrolase EF_0837/AHA_3915; Region: EF_0837; TIGR03583 998088001022 Metallo-dependent hydrolases, subgroup B is part of the superfamily of metallo-dependent hydrolases, 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...; Region: Met_dep_hydrolase_B; cd01307 998088001023 active site 998088001024 conserved hypothetical protein EF_0833/AHA_3914; Region: EF_0833; TIGR03579 998088001025 Domain of unknown function (DUF4311); Region: DUF4311; cl11919 998088001026 conserved hypothetical protein EF_0831/AHA_3912; Region: EF_0831; TIGR03578 998088001027 conserved hypothetical protein EF_0830/AHA_3911; Region: EF_0830; TIGR03577 998088001028 PRD domain protein EF_0829/AHA_3910; Region: EF_0829; TIGR03582 998088001029 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 998088001030 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 998088001031 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 998088001032 protein binding site [polypeptide binding]; other site 998088001033 serine endoprotease; Provisional; Region: PRK10942 998088001034 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 998088001035 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 998088001036 protein binding site [polypeptide binding]; other site 998088001037 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 998088001038 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 998088001039 Predicted ATPase [General function prediction only]; Region: COG1485 998088001040 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 998088001041 23S rRNA interface [nucleotide binding]; other site 998088001042 L3 interface [polypeptide binding]; other site 998088001043 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 998088001044 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 998088001045 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 998088001046 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 998088001047 [2Fe-2S] cluster binding site [ion binding]; other site 998088001048 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 998088001049 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 998088001050 Qi binding site; other site 998088001051 intrachain domain interface; other site 998088001052 interchain domain interface [polypeptide binding]; other site 998088001053 heme bH binding site [chemical binding]; other site 998088001054 heme bL binding site [chemical binding]; other site 998088001055 Qo binding site; other site 998088001056 interchain domain interface [polypeptide binding]; other site 998088001057 intrachain domain interface; other site 998088001058 Qi binding site; other site 998088001059 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 998088001060 Qo binding site; other site 998088001061 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 998088001062 stringent starvation protein A; Provisional; Region: sspA; PRK09481 998088001063 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 998088001064 C-terminal domain interface [polypeptide binding]; other site 998088001065 putative GSH binding site (G-site) [chemical binding]; other site 998088001066 dimer interface [polypeptide binding]; other site 998088001067 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 998088001068 dimer interface [polypeptide binding]; other site 998088001069 N-terminal domain interface [polypeptide binding]; other site 998088001070 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 998088001071 BON domain; Region: BON; pfam04972 998088001072 BON domain; Region: BON; pfam04972 998088001073 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 998088001074 dimer interface [polypeptide binding]; other site 998088001075 active site 998088001076 hypothetical protein; Reviewed; Region: PRK12497 998088001077 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 998088001078 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 998088001079 putative ligand binding site [chemical binding]; other site 998088001080 Predicted methyltransferases [General function prediction only]; Region: COG0313 998088001081 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 998088001082 putative SAM binding site [chemical binding]; other site 998088001083 putative homodimer interface [polypeptide binding]; other site 998088001084 cell division protein MraZ; Reviewed; Region: PRK00326 998088001085 MraZ protein; Region: MraZ; pfam02381 998088001086 MraZ protein; Region: MraZ; pfam02381 998088001087 MraW methylase family; Region: Methyltransf_5; pfam01795 998088001088 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 998088001089 Cell division protein FtsL; Region: FtsL; pfam04999 998088001090 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 998088001091 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 998088001092 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 998088001093 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 998088001094 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 998088001095 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001096 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001097 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 998088001098 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 998088001099 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001100 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001101 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 998088001102 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 998088001103 Mg++ binding site [ion binding]; other site 998088001104 putative catalytic motif [active] 998088001105 putative substrate binding site [chemical binding]; other site 998088001106 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03806 998088001107 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001108 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001109 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 998088001110 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 998088001111 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 998088001112 active site 998088001113 homodimer interface [polypeptide binding]; other site 998088001114 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 998088001115 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 998088001116 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088001117 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088001118 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 998088001119 Cell division protein FtsQ; Region: FtsQ; pfam03799 998088001120 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 998088001121 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 998088001122 nucleotide binding site [chemical binding]; other site 998088001123 Cell division protein FtsA; Region: FtsA; pfam14450 998088001124 cell division protein FtsZ; Validated; Region: PRK09330 998088001125 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 998088001126 nucleotide binding site [chemical binding]; other site 998088001127 SulA interaction site; other site 998088001128 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 998088001129 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 998088001130 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088001131 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 998088001132 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 998088001133 SEC-C motif; Region: SEC-C; pfam02810 998088001134 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 998088001135 active site 998088001136 8-oxo-dGMP binding site [chemical binding]; other site 998088001137 nudix motif; other site 998088001138 metal binding site [ion binding]; metal-binding site 998088001139 Domain of unknown function (DUF329); Region: DUF329; cl01144 998088001140 hypothetical protein; Provisional; Region: PRK05287 998088001141 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 998088001142 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 998088001143 CoA-binding site [chemical binding]; other site 998088001144 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 998088001145 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 998088001146 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 998088001147 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 998088001148 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 998088001149 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 998088001150 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 998088001151 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 998088001152 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 998088001153 Walker A motif; other site 998088001154 ATP binding site [chemical binding]; other site 998088001155 Walker B motif; other site 998088001156 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 998088001157 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 998088001158 dimerization interface [polypeptide binding]; other site 998088001159 active site 998088001160 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 998088001161 catalytic motif [active] 998088001162 Catalytic residue [active] 998088001163 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 998088001164 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 998088001165 substrate binding site [chemical binding]; other site 998088001166 amidase catalytic site [active] 998088001167 Zn binding residues [ion binding]; other site 998088001168 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 998088001169 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088001170 DNA-binding site [nucleotide binding]; DNA binding site 998088001171 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 998088001172 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 998088001173 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 998088001174 dimer interface [polypeptide binding]; other site 998088001175 TPP-binding site [chemical binding]; other site 998088001176 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 998088001177 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 998088001178 E3 interaction surface; other site 998088001179 lipoyl attachment site [posttranslational modification]; other site 998088001180 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 998088001181 E3 interaction surface; other site 998088001182 lipoyl attachment site [posttranslational modification]; other site 998088001183 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 998088001184 E3 interaction surface; other site 998088001185 lipoyl attachment site [posttranslational modification]; other site 998088001186 e3 binding domain; Region: E3_binding; pfam02817 998088001187 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 998088001188 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 998088001189 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088001190 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088001191 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088001192 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 998088001193 GAF domain; Region: GAF; pfam01590 998088001194 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088001195 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001196 metal binding site [ion binding]; metal-binding site 998088001197 active site 998088001198 I-site; other site 998088001199 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 998088001200 dimerization interface [polypeptide binding]; other site 998088001201 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088001202 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088001203 dimer interface [polypeptide binding]; other site 998088001204 putative CheW interface [polypeptide binding]; other site 998088001205 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 998088001206 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 998088001207 active site 998088001208 nucleophile elbow; other site 998088001209 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 998088001210 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 998088001211 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 998088001212 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 998088001213 substrate binding site [chemical binding]; other site 998088001214 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 998088001215 substrate binding site [chemical binding]; other site 998088001216 ligand binding site [chemical binding]; other site 998088001217 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 998088001218 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 998088001219 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 998088001220 FAD-linked oxidoreductase; Region: bact_FAD_ox; TIGR01679 998088001221 FAD binding domain; Region: FAD_binding_4; pfam01565 998088001222 D-arabinono-1,4-lactone oxidase; Region: ALO; pfam04030 998088001223 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 998088001224 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 998088001225 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 998088001226 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 998088001227 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088001228 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088001229 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088001230 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088001231 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 998088001232 putative transporter; Provisional; Region: PRK10504 998088001233 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 998088001234 putative substrate translocation pore; other site 998088001235 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 998088001236 putative deacylase active site [active] 998088001237 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 998088001238 catalytic center binding site [active] 998088001239 ATP binding site [chemical binding]; other site 998088001240 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 998088001241 homooctamer interface [polypeptide binding]; other site 998088001242 active site 998088001243 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 998088001244 Nucleoside recognition; Region: Gate; pfam07670 998088001245 Protein of unknown function (DUF1706); Region: DUF1706; pfam08020 998088001246 argininosuccinate lyase; Provisional; Region: PRK04833 998088001247 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 998088001248 active sites [active] 998088001249 tetramer interface [polypeptide binding]; other site 998088001250 argininosuccinate synthase; Provisional; Region: PRK13820 998088001251 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 998088001252 ANP binding site [chemical binding]; other site 998088001253 Substrate Binding Site II [chemical binding]; other site 998088001254 Substrate Binding Site I [chemical binding]; other site 998088001255 ornithine carbamoyltransferase; Provisional; Region: PRK14805 998088001256 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 998088001257 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 998088001258 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 998088001259 nucleotide binding site [chemical binding]; other site 998088001260 substrate binding site [chemical binding]; other site 998088001261 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 998088001262 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 998088001263 acetylornithine deacetylase; Provisional; Region: PRK05111 998088001264 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 998088001265 metal binding site [ion binding]; metal-binding site 998088001266 putative dimer interface [polypeptide binding]; other site 998088001267 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 998088001268 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 998088001269 PAS fold; Region: PAS_4; pfam08448 998088001270 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088001271 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001272 metal binding site [ion binding]; metal-binding site 998088001273 active site 998088001274 I-site; other site 998088001275 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088001276 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 998088001277 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 998088001278 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 998088001279 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088001280 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001281 metal binding site [ion binding]; metal-binding site 998088001282 active site 998088001283 I-site; other site 998088001284 ammonium transporter; Provisional; Region: PRK10666 998088001285 Outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]; Region: SlyB; COG3133 998088001286 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 998088001287 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088001288 Coenzyme A binding pocket [chemical binding]; other site 998088001289 Nitrous oxide-stimulated promoter; Region: YgbA_NO; cl08119 998088001290 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 998088001291 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 998088001292 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 998088001293 active site 998088001294 Transcriptional regulators [Transcription]; Region: GntR; COG1802 998088001295 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088001296 DNA-binding site [nucleotide binding]; DNA binding site 998088001297 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 998088001298 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 998088001299 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_ATP; cd00484 998088001300 active site 998088001301 substrate-binding site [chemical binding]; other site 998088001302 metal-binding site [ion binding] 998088001303 ATP binding site [chemical binding]; other site 998088001304 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 998088001305 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 998088001306 dimerization interface [polypeptide binding]; other site 998088001307 domain crossover interface; other site 998088001308 redox-dependent activation switch; other site 998088001309 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 998088001310 RNA binding surface [nucleotide binding]; other site 998088001311 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 998088001312 nudix motif; other site 998088001313 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 998088001314 active site 998088001315 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 998088001316 Integrase core domain; Region: rve_3; pfam13683 998088001317 DNA-binding transcriptional regulator DhaR; Provisional; Region: PRK11388 998088001318 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 998088001319 Walker A motif; other site 998088001320 ATP binding site [chemical binding]; other site 998088001321 Walker B motif; other site 998088001322 arginine finger; other site 998088001323 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 998088001324 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 998088001325 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 998088001326 dimer interface [polypeptide binding]; other site 998088001327 active site 998088001328 metal binding site [ion binding]; metal-binding site 998088001329 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 998088001330 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 998088001331 dimerization domain swap beta strand [polypeptide binding]; other site 998088001332 regulatory protein interface [polypeptide binding]; other site 998088001333 active site 998088001334 regulatory phosphorylation site [posttranslational modification]; other site 998088001335 DAK2 domain; Region: Dak2; cl03685 998088001336 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK11468 998088001337 Dak1 domain; Region: Dak1; pfam02733 998088001338 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 998088001339 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 998088001340 DNA-binding site [nucleotide binding]; DNA binding site 998088001341 RNA-binding motif; other site 998088001342 YjbD family (DUF3811); Region: DUF3811; cl08125 998088001343 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 998088001344 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 998088001345 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 998088001346 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088001347 substrate binding pocket [chemical binding]; other site 998088001348 membrane-bound complex binding site; other site 998088001349 hinge residues; other site 998088001350 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 998088001351 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 998088001352 dimer interface [polypeptide binding]; other site 998088001353 ssDNA binding site [nucleotide binding]; other site 998088001354 tetramer (dimer of dimers) interface [polypeptide binding]; other site 998088001355 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 998088001356 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 998088001357 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 998088001358 DNA binding residues [nucleotide binding] 998088001359 dimerization interface [polypeptide binding]; other site 998088001360 Curli assembly protein CsgE; Region: CsgE; pfam10627 998088001361 Type VIII secretion system (T8SS), CsgF protein; Region: CsgF; pfam10614 998088001362 Curli production assembly/transport component CsgG; Region: CsgG; cl17434 998088001363 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 998088001364 major curlin subunit; Provisional; Region: csgA; PRK10051 998088001365 major curlin subunit; Provisional; Region: csgA; PRK10051 998088001366 major curlin subunit; Provisional; Region: csgA; PRK10051 998088001367 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 998088001368 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 998088001369 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 998088001370 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 998088001371 CHASE4 domain; Region: CHASE4; pfam05228 998088001372 HAMP domain; Region: HAMP; pfam00672 998088001373 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088001374 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001375 metal binding site [ion binding]; metal-binding site 998088001376 active site 998088001377 I-site; other site 998088001378 outer membrane protein W; Provisional; Region: PRK10959 998088001379 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088001380 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088001381 HAMP domain; Region: HAMP; pfam00672 998088001382 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088001383 dimer interface [polypeptide binding]; other site 998088001384 putative CheW interface [polypeptide binding]; other site 998088001385 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 998088001386 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 998088001387 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 998088001388 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 998088001389 FAD binding site [chemical binding]; other site 998088001390 Protein of unknown function (DUF3103); Region: DUF3103; pfam11301 998088001391 Benzoate membrane transport protein; Region: BenE; pfam03594 998088001392 benzoate transporter; Region: benE; TIGR00843 998088001393 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 998088001394 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 998088001395 non-specific DNA binding site [nucleotide binding]; other site 998088001396 salt bridge; other site 998088001397 sequence-specific DNA binding site [nucleotide binding]; other site 998088001398 Cupin domain; Region: Cupin_2; pfam07883 998088001399 NnrS protein; Region: NnrS; pfam05940 998088001400 hypothetical protein; Provisional; Region: PRK05423 998088001401 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 998088001402 Transglycosylase; Region: Transgly; cl17702 998088001403 sugar phosphate phosphatase; Provisional; Region: PRK10513 998088001404 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 998088001405 active site 998088001406 motif I; other site 998088001407 motif II; other site 998088001408 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 998088001409 Protein of unknown function (DUF342); Region: DUF342; pfam03961 998088001410 hypothetical protein; Provisional; Region: PRK03673 998088001411 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 998088001412 putative MPT binding site; other site 998088001413 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 998088001414 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 998088001415 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088001416 Zn2+ binding site [ion binding]; other site 998088001417 Mg2+ binding site [ion binding]; other site 998088001418 homoserine O-succinyltransferase; Provisional; Region: PRK05368 998088001419 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 998088001420 proposed active site lysine [active] 998088001421 conserved cys residue [active] 998088001422 Predicted protein-tyrosine phosphatase [Signal transduction mechanisms]; Region: CDC14; COG2453 998088001423 active site 998088001424 catalytic residues [active] 998088001425 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 998088001426 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 998088001427 putative DNA binding site [nucleotide binding]; other site 998088001428 putative Zn2+ binding site [ion binding]; other site 998088001429 AsnC family; Region: AsnC_trans_reg; pfam01037 998088001430 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 998088001431 Sulfatase; Region: Sulfatase; pfam00884 998088001432 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 998088001433 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 998088001434 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 998088001435 N-terminal plug; other site 998088001436 ligand-binding site [chemical binding]; other site 998088001437 Alpha amylase catalytic domain family; Region: AmyAc_family; cd00551 998088001438 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 998088001439 active site 998088001440 catalytic site [active] 998088001441 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 998088001442 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 998088001443 ATP-grasp domain; Region: ATP-grasp_4; cl17255 998088001444 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 998088001445 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088001446 Coenzyme A binding pocket [chemical binding]; other site 998088001447 Protein of unknown function (DUF3624); Region: DUF3624; pfam12292 998088001448 malonic semialdehyde reductase; Provisional; Region: PRK10538 998088001449 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001450 NAD(P) binding site [chemical binding]; other site 998088001451 active site 998088001452 Peptidase family C69; Region: Peptidase_C69; cl17793 998088001453 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 998088001454 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 998088001455 dimer interface [polypeptide binding]; other site 998088001456 active site 998088001457 metal binding site [ion binding]; metal-binding site 998088001458 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 998088001459 active site 998088001460 dimer interfaces [polypeptide binding]; other site 998088001461 catalytic residues [active] 998088001462 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 998088001463 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 998088001464 heme binding site [chemical binding]; other site 998088001465 ferroxidase pore; other site 998088001466 ferroxidase diiron center [ion binding]; other site 998088001467 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 998088001468 Transcriptional activator HlyU; Region: HlyU; pfam10115 998088001469 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088001470 NAD(P) binding site [chemical binding]; other site 998088001471 active site 998088001472 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 998088001473 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088001474 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 998088001475 active site 998088001476 phosphorylation site [posttranslational modification] 998088001477 intermolecular recognition site; other site 998088001478 dimerization interface [polypeptide binding]; other site 998088001479 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 998088001480 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 998088001481 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 998088001482 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 998088001483 putative active site [active] 998088001484 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 998088001485 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 998088001486 putative fimbrial outer membrane usher protein StfC; Provisional; Region: PRK15284 998088001487 PapC N-terminal domain; Region: PapC_N; pfam13954 998088001488 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 998088001489 PapC C-terminal domain; Region: PapC_C; pfam13953 998088001490 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 998088001491 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 998088001492 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 998088001493 Fimbrial protein; Region: Fimbrial; cl01416 998088001494 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 998088001495 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088001496 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 998088001497 DNA binding site [nucleotide binding] 998088001498 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 998088001499 O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE); Region: OSB_CoA_lg; cd05912 998088001500 acyl-activating enzyme (AAE) consensus motif; other site 998088001501 putative AMP binding site [chemical binding]; other site 998088001502 putative active site [active] 998088001503 putative CoA binding site [chemical binding]; other site 998088001504 O-succinylbenzoate synthase; Provisional; Region: PRK05105 998088001505 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway; Region: OSBS; cd03320 998088001506 active site 998088001507 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 998088001508 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 998088001509 substrate binding site [chemical binding]; other site 998088001510 oxyanion hole (OAH) forming residues; other site 998088001511 trimer interface [polypeptide binding]; other site 998088001512 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 998088001513 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 998088001514 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 998088001515 dimer interface [polypeptide binding]; other site 998088001516 tetramer interface [polypeptide binding]; other site 998088001517 PYR/PP interface [polypeptide binding]; other site 998088001518 TPP binding site [chemical binding]; other site 998088001519 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 998088001520 TPP-binding site; other site 998088001521 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 998088001522 chorismate binding enzyme; Region: Chorismate_bind; cl10555 998088001523 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 998088001524 UbiA prenyltransferase family; Region: UbiA; pfam01040 998088001525 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 998088001526 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 998088001527 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 998088001528 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 998088001529 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 998088001530 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 998088001531 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 998088001532 ATP binding site [chemical binding]; other site 998088001533 Mg++ binding site [ion binding]; other site 998088001534 motif III; other site 998088001535 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 998088001536 nucleotide binding region [chemical binding]; other site 998088001537 ATP-binding site [chemical binding]; other site 998088001538 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 998088001539 putative RNA binding site [nucleotide binding]; other site 998088001540 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 998088001541 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 998088001542 Nucleoside recognition; Region: Gate; pfam07670 998088001543 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 998088001544 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 998088001545 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 998088001546 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 998088001547 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 998088001548 Cl binding site [ion binding]; other site 998088001549 oligomer interface [polypeptide binding]; other site 998088001550 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 998088001551 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088001552 DNA-J related protein; Region: DNAJ_related; pfam12339 998088001553 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 998088001554 HSP70 interaction site [polypeptide binding]; other site 998088001555 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 998088001556 TrkA-N domain; Region: TrkA_N; pfam02254 998088001557 Transcriptional regulator [Transcription]; Region: MtlR; COG3722 998088001558 mannitol repressor protein; Provisional; Region: mtlR; PRK11001 998088001559 mannitol-1-phosphate 5-dehydrogenase; Provisional; Region: PRK02318 998088001560 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 998088001561 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 998088001562 PTS system mannitol-specific transporter subunit IICBA; Provisional; Region: PRK15083 998088001563 PTS system, mannitol-specific IIC component; Region: mtlA; TIGR00851 998088001564 PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane...; Region: PTS_IIB_mannitol; cd05567 998088001565 active site 998088001566 P-loop; other site 998088001567 phosphorylation site [posttranslational modification] 998088001568 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 998088001569 active site 998088001570 phosphorylation site [posttranslational modification] 998088001571 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 998088001572 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 998088001573 putative acyl-acceptor binding pocket; other site 998088001574 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 998088001575 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 998088001576 putative ribose interaction site [chemical binding]; other site 998088001577 putative ADP binding site [chemical binding]; other site 998088001578 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 998088001579 active site 998088001580 nucleotide binding site [chemical binding]; other site 998088001581 HIGH motif; other site 998088001582 KMSKS motif; other site 998088001583 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 998088001584 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 998088001585 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 998088001586 dimer interface [polypeptide binding]; other site 998088001587 ADP-ribose binding site [chemical binding]; other site 998088001588 active site 998088001589 nudix motif; other site 998088001590 metal binding site [ion binding]; metal-binding site 998088001591 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 998088001592 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 998088001593 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 998088001594 active site 998088001595 metal binding site [ion binding]; metal-binding site 998088001596 hexamer interface [polypeptide binding]; other site 998088001597 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 998088001598 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 998088001599 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 998088001600 ATP binding site [chemical binding]; other site 998088001601 Mg2+ binding site [ion binding]; other site 998088001602 G-X-G motif; other site 998088001603 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 998088001604 anchoring element; other site 998088001605 dimer interface [polypeptide binding]; other site 998088001606 ATP binding site [chemical binding]; other site 998088001607 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 998088001608 active site 998088001609 metal binding site [ion binding]; metal-binding site 998088001610 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 998088001611 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 998088001612 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 998088001613 CAP-like domain; other site 998088001614 active site 998088001615 primary dimer interface [polypeptide binding]; other site 998088001616 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088001617 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088001618 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 998088001619 putative effector binding pocket; other site 998088001620 dimerization interface [polypeptide binding]; other site 998088001621 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 998088001622 Major Facilitator Superfamily; Region: MFS_1; pfam07690 998088001623 putative substrate translocation pore; other site 998088001624 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 998088001625 amino acid/peptide transporter (Peptide:H+ symporter), bacterial; Region: yjdL_sub1_fam; TIGR00924 998088001626 POT family; Region: PTR2; cl17359 998088001627 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 998088001628 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 998088001629 HSP70 interaction site [polypeptide binding]; other site 998088001630 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 998088001631 classical (c) SDRs; Region: SDR_c; cd05233 998088001632 NAD(P) binding site [chemical binding]; other site 998088001633 active site 998088001634 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 998088001635 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 998088001636 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088001637 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088001638 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 998088001639 TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif; Region: TlpA_like_ScsD_MtbDsbE; cd03011 998088001640 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 998088001641 catalytic residues [active] 998088001642 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 998088001643 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 998088001644 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 998088001645 catalytic residues [active] 998088001646 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 998088001647 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 998088001648 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 998088001649 DsbD alpha interface [polypeptide binding]; other site 998088001650 catalytic residues [active] 998088001651 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 998088001652 putative acyl-acceptor binding pocket; other site 998088001653 phage shock protein A; Region: phageshock_pspA; TIGR02977 998088001654 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 998088001655 GIY-YIG motif/motif A; other site 998088001656 putative active site [active] 998088001657 putative metal binding site [ion binding]; other site 998088001658 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088001659 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 998088001660 substrate binding pocket [chemical binding]; other site 998088001661 membrane-bound complex binding site; other site 998088001662 hinge residues; other site 998088001663 Predicted permeases [General function prediction only]; Region: RarD; COG2962 998088001664 EamA-like transporter family; Region: EamA; pfam00892 998088001665 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 998088001666 putative uracil binding site [chemical binding]; other site 998088001667 putative active site [active] 998088001668 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088001669 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 998088001670 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088001671 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 998088001672 dimerization interface [polypeptide binding]; other site 998088001673 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 998088001674 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 998088001675 ABC-ATPase subunit interface; other site 998088001676 dimer interface [polypeptide binding]; other site 998088001677 putative PBP binding regions; other site 998088001678 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 998088001679 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 998088001680 high-affinity zinc transporter periplasmic component; Reviewed; Region: znuA; PRK09545 998088001681 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 998088001682 metal binding site [ion binding]; metal-binding site 998088001683 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 998088001684 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 998088001685 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 998088001686 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 998088001687 putative peptidase; Provisional; Region: PRK11649 998088001688 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 998088001689 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088001690 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 998088001691 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 998088001692 NAD binding site [chemical binding]; other site 998088001693 ligand binding site [chemical binding]; other site 998088001694 catalytic site [active] 998088001695 Protein of unknown function (DUF416); Region: DUF416; pfam04222 998088001696 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 998088001697 MarR family; Region: MarR; pfam01047 998088001698 MarR family; Region: MarR_2; cl17246 998088001699 BCCT family transporter; Region: BCCT; pfam02028 998088001700 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 998088001701 Poly A polymerase head domain; Region: PolyA_pol; pfam01743 998088001702 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 998088001703 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088001704 Zn2+ binding site [ion binding]; other site 998088001705 Mg2+ binding site [ion binding]; other site 998088001706 adenine DNA glycosylase; Provisional; Region: PRK10880 998088001707 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 998088001708 minor groove reading motif; other site 998088001709 helix-hairpin-helix signature motif; other site 998088001710 substrate binding pocket [chemical binding]; other site 998088001711 active site 998088001712 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 998088001713 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 998088001714 DNA binding and oxoG recognition site [nucleotide binding] 998088001715 oxidative damage protection protein; Provisional; Region: PRK05408 998088001716 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 998088001717 murein transglycosylase C; Provisional; Region: mltC; PRK11671 998088001718 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 998088001719 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088001720 catalytic residue [active] 998088001721 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 998088001722 Fatty acyltransferase-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: fatty_acyltransferase_like; cd01846 998088001723 active site 998088001724 catalytic triad [active] 998088001725 oxyanion hole [active] 998088001726 outer membrane protein A; Reviewed; Region: PRK10808 998088001727 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 998088001728 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088001729 ligand binding site [chemical binding]; other site 998088001730 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088001731 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001732 metal binding site [ion binding]; metal-binding site 998088001733 active site 998088001734 I-site; other site 998088001735 exoribonuclease R; Provisional; Region: PRK11642 998088001736 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 998088001737 RNB domain; Region: RNB; pfam00773 998088001738 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 998088001739 RNA binding site [nucleotide binding]; other site 998088001740 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 998088001741 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 998088001742 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 998088001743 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 998088001744 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 998088001745 ligand binding site [chemical binding]; other site 998088001746 Predicted acyltransferase [General function prediction only]; Region: ElaA; COG2153 998088001747 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 998088001748 DEAD-like helicases superfamily; Region: DEXDc; smart00487 998088001749 ATP binding site [chemical binding]; other site 998088001750 Mg++ binding site [ion binding]; other site 998088001751 motif III; other site 998088001752 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 998088001753 nucleotide binding region [chemical binding]; other site 998088001754 ATP-binding site [chemical binding]; other site 998088001755 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 998088001756 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 998088001757 S-adenosylmethionine binding site [chemical binding]; other site 998088001758 Branched-chain amino acid transport protein; Region: Branch_AA_trans; pfam05525 998088001759 Branched-chain amino acid transport protein; Region: Branch_AA_trans; pfam05525 998088001760 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 998088001761 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 998088001762 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 998088001763 metal binding site 2 [ion binding]; metal-binding site 998088001764 putative DNA binding helix; other site 998088001765 metal binding site 1 [ion binding]; metal-binding site 998088001766 dimer interface [polypeptide binding]; other site 998088001767 structural Zn2+ binding site [ion binding]; other site 998088001768 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 998088001769 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 998088001770 FMN binding site [chemical binding]; other site 998088001771 active site 998088001772 catalytic residues [active] 998088001773 substrate binding site [chemical binding]; other site 998088001774 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 998088001775 PAS domain; Region: PAS_9; pfam13426 998088001776 putative active site [active] 998088001777 heme pocket [chemical binding]; other site 998088001778 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088001779 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088001780 dimer interface [polypeptide binding]; other site 998088001781 putative CheW interface [polypeptide binding]; other site 998088001782 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 998088001783 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 998088001784 peptide binding site [polypeptide binding]; other site 998088001785 Putative ParB-like nuclease; Region: ParBc_2; cl17538 998088001786 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 998088001787 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 998088001788 trimer interface [polypeptide binding]; other site 998088001789 active site 998088001790 substrate binding site [chemical binding]; other site 998088001791 CoA binding site [chemical binding]; other site 998088001792 Protein of unknown function (DUF2753); Region: DUF2753; pfam10952 998088001793 enoyl-CoA hydratase; Provisional; Region: PRK06688 998088001794 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 998088001795 substrate binding site [chemical binding]; other site 998088001796 oxyanion hole (OAH) forming residues; other site 998088001797 trimer interface [polypeptide binding]; other site 998088001798 Protein of unknown function (DUF461); Region: DUF461; pfam04314 998088001799 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 998088001800 3-ketodihydrosphingosine reductase (KDSR) and related proteins, classical (c) SDR; Region: KDSR-like_SDR_c; cd08939 998088001801 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 998088001802 putative NAD(P) binding site [chemical binding]; other site 998088001803 homotetramer interface [polypeptide binding]; other site 998088001804 active site 998088001805 homodimer interface [polypeptide binding]; other site 998088001806 prolyl-tRNA synthetase; Provisional; Region: PRK09194 998088001807 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 998088001808 dimer interface [polypeptide binding]; other site 998088001809 motif 1; other site 998088001810 active site 998088001811 motif 2; other site 998088001812 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 998088001813 putative deacylase active site [active] 998088001814 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 998088001815 active site 998088001816 motif 3; other site 998088001817 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 998088001818 anticodon binding site; other site 998088001819 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 998088001820 TRAM domain; Region: TRAM; pfam01938 998088001821 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 998088001822 S-adenosylmethionine binding site [chemical binding]; other site 998088001823 Protein of unknown function (DUF330); Region: DUF330; pfam03886 998088001824 paraquat-inducible protein B; Provisional; Region: PRK10807 998088001825 mce related protein; Region: MCE; pfam02470 998088001826 mce related protein; Region: MCE; pfam02470 998088001827 paraquat-inducible membrane protein A; Provisional; Region: PRK15103 998088001828 Paraquat-inducible protein A; Region: PqiA; pfam04403 998088001829 Paraquat-inducible protein A; Region: PqiA; pfam04403 998088001830 bacterial Hfq-like; Region: Hfq; cd01716 998088001831 hexamer interface [polypeptide binding]; other site 998088001832 Sm1 motif; other site 998088001833 RNA binding site [nucleotide binding]; other site 998088001834 Sm2 motif; other site 998088001835 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 998088001836 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 998088001837 motif II; other site 998088001838 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 998088001839 GAF domain; Region: GAF_3; pfam13492 998088001840 GAF domain; Region: GAF; cl17456 998088001841 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088001842 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088001843 metal binding site [ion binding]; metal-binding site 998088001844 active site 998088001845 I-site; other site 998088001846 exoribonuclease II; Provisional; Region: PRK05054 998088001847 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 998088001848 RNB domain; Region: RNB; pfam00773 998088001849 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 998088001850 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088001851 The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; Region: PBP2_IciA_ArgP; cd08428 998088001852 putative dimerization interface [polypeptide binding]; other site 998088001853 Autoinducer synthetase; Region: Autoind_synth; cl17404 998088001854 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 998088001855 Autoinducer binding domain; Region: Autoind_bind; pfam03472 998088001856 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 998088001857 DNA binding residues [nucleotide binding] 998088001858 dimerization interface [polypeptide binding]; other site 998088001859 L-lysine exporter; Region: 2a75; TIGR00948 998088001860 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088001861 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 998088001862 dimerization interface [polypeptide binding]; other site 998088001863 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088001864 dimer interface [polypeptide binding]; other site 998088001865 putative CheW interface [polypeptide binding]; other site 998088001866 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 998088001867 RuvA N terminal domain; Region: RuvA_N; pfam01330 998088001868 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 998088001869 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 998088001870 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 998088001871 Walker A motif; other site 998088001872 ATP binding site [chemical binding]; other site 998088001873 Walker B motif; other site 998088001874 arginine finger; other site 998088001875 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 998088001876 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 998088001877 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 998088001878 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 998088001879 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 998088001880 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 998088001881 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; pfam09600 998088001882 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 998088001883 active site 998088001884 TolQ protein; Region: tolQ; TIGR02796 998088001885 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 998088001886 TolR protein; Region: tolR; TIGR02801 998088001887 TolA protein; Region: tolA_full; TIGR02794 998088001888 TolA C-terminal; Region: TolA; pfam06519 998088001889 translocation protein TolB; Provisional; Region: tolB; PRK04792 998088001890 TolB amino-terminal domain; Region: TolB_N; pfam04052 998088001891 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 998088001892 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 998088001893 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 998088001894 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 998088001895 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088001896 ligand binding site [chemical binding]; other site 998088001897 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 998088001898 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 998088001899 binding surface 998088001900 TPR motif; other site 998088001901 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 998088001902 Na2 binding site [ion binding]; other site 998088001903 putative substrate binding site 1 [chemical binding]; other site 998088001904 Na binding site 1 [ion binding]; other site 998088001905 putative substrate binding site 2 [chemical binding]; other site 998088001906 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088001907 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 998088001908 substrate binding pocket [chemical binding]; other site 998088001909 membrane-bound complex binding site; other site 998088001910 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 998088001911 Na2 binding site [ion binding]; other site 998088001912 putative substrate binding site 1 [chemical binding]; other site 998088001913 Na binding site 1 [ion binding]; other site 998088001914 putative substrate binding site 2 [chemical binding]; other site 998088001915 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 998088001916 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 998088001917 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 998088001918 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 998088001919 pyridoxal phosphate (PLP) phosphatase; Provisional; Region: PRK10530 998088001920 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 998088001921 active site 998088001922 motif I; other site 998088001923 motif II; other site 998088001924 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 998088001925 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 998088001926 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 998088001927 putative substrate translocation pore; other site 998088001928 Predicted transcriptional regulator [Transcription]; Region: COG2345 998088001929 MarR family; Region: MarR_2; cl17246 998088001930 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 998088001931 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 998088001932 putative DNA binding site [nucleotide binding]; other site 998088001933 putative Zn2+ binding site [ion binding]; other site 998088001934 AsnC family; Region: AsnC_trans_reg; pfam01037 998088001935 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 998088001936 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_19; cd04678 998088001937 nudix motif; other site 998088001938 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 998088001939 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 998088001940 Chromate transporter; Region: Chromate_transp; pfam02417 998088001941 methionine sulfoxide reductase B; Provisional; Region: PRK00222 998088001942 SelR domain; Region: SelR; pfam01641 998088001943 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 998088001944 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 998088001945 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 998088001946 active site 998088001947 catalytic site [active] 998088001948 glycogen branching enzyme; Provisional; Region: PRK05402 998088001949 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 998088001950 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 998088001951 active site 998088001952 catalytic site [active] 998088001953 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 998088001954 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 998088001955 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 998088001956 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 998088001957 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 998088001958 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 998088001959 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 998088001960 active site 998088001961 phosphate binding residues; other site 998088001962 catalytic residues [active] 998088001963 quinolinate synthetase; Provisional; Region: PRK09375 998088001964 HAMP domain; Region: HAMP; pfam00672 998088001965 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088001966 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088001967 dimer interface [polypeptide binding]; other site 998088001968 putative CheW interface [polypeptide binding]; other site 998088001969 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 998088001970 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 998088001971 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 998088001972 siroheme synthase; Provisional; Region: cysG; PRK10637 998088001973 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 998088001974 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 998088001975 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 998088001976 active site 998088001977 SAM binding site [chemical binding]; other site 998088001978 homodimer interface [polypeptide binding]; other site 998088001979 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 998088001980 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 998088001981 Active Sites [active] 998088001982 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 998088001983 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 998088001984 CysD dimerization site [polypeptide binding]; other site 998088001985 G1 box; other site 998088001986 putative GEF interaction site [polypeptide binding]; other site 998088001987 GTP/Mg2+ binding site [chemical binding]; other site 998088001988 Switch I region; other site 998088001989 G2 box; other site 998088001990 G3 box; other site 998088001991 Switch II region; other site 998088001992 G4 box; other site 998088001993 G5 box; other site 998088001994 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 998088001995 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 998088001996 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 998088001997 TrkA-C domain; Region: TrkA_C; pfam02080 998088001998 TrkA-C domain; Region: TrkA_C; pfam02080 998088001999 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 998088002000 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 998088002001 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 998088002002 ligand-binding site [chemical binding]; other site 998088002003 FRG domain; Region: FRG; pfam08867 998088002004 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 998088002005 PAS fold; Region: PAS_3; pfam08447 998088002006 putative active site [active] 998088002007 heme pocket [chemical binding]; other site 998088002008 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088002009 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088002010 dimer interface [polypeptide binding]; other site 998088002011 putative CheW interface [polypeptide binding]; other site 998088002012 TIGR03899 family protein; Region: TIGR03899 998088002013 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 998088002014 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088002015 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 998088002016 FtsX-like permease family; Region: FtsX; pfam02687 998088002017 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 998088002018 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 998088002019 Walker A/P-loop; other site 998088002020 ATP binding site [chemical binding]; other site 998088002021 Q-loop/lid; other site 998088002022 ABC transporter signature motif; other site 998088002023 Walker B; other site 998088002024 D-loop; other site 998088002025 H-loop/switch region; other site 998088002026 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 998088002027 Bacterial protein of unknown function (YtfJ_HI0045); Region: YtfJ_HI0045; pfam09695 998088002028 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 998088002029 dimer interface [polypeptide binding]; other site 998088002030 substrate binding site [chemical binding]; other site 998088002031 metal binding sites [ion binding]; metal-binding site 998088002032 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 998088002033 active site 998088002034 phosphorylation site [posttranslational modification] 998088002035 intermolecular recognition site; other site 998088002036 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 998088002037 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088002038 Zn2+ binding site [ion binding]; other site 998088002039 Mg2+ binding site [ion binding]; other site 998088002040 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002041 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088002042 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 998088002043 dimerization interface [polypeptide binding]; other site 998088002044 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 998088002045 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 998088002046 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_1; cd08352 998088002047 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 998088002048 putative metal binding site [ion binding]; other site 998088002049 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 998088002050 Transglycosylase; Region: Transgly; pfam00912 998088002051 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 998088002052 ATP-dependent RNA helicase HrpB; Provisional; Region: PRK11664 998088002053 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 998088002054 ATP binding site [chemical binding]; other site 998088002055 putative Mg++ binding site [ion binding]; other site 998088002056 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 998088002057 nucleotide binding region [chemical binding]; other site 998088002058 ATP-binding site [chemical binding]; other site 998088002059 Helicase associated domain (HA2); Region: HA2; cl04503 998088002060 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 998088002061 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 998088002062 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 998088002063 RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]; Region: KptA; COG1859 998088002064 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 998088002065 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 998088002066 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 998088002067 active site 998088002068 nucleotide binding site [chemical binding]; other site 998088002069 HIGH motif; other site 998088002070 KMSKS motif; other site 998088002071 poly(A) polymerase I; Provisional; Region: pcnB; PRK11623 998088002072 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 998088002073 active site 998088002074 NTP binding site [chemical binding]; other site 998088002075 metal binding triad [ion binding]; metal-binding site 998088002076 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 998088002077 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 998088002078 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 998088002079 catalytic center binding site [active] 998088002080 ATP binding site [chemical binding]; other site 998088002081 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 998088002082 oligomerization interface [polypeptide binding]; other site 998088002083 active site 998088002084 metal binding site [ion binding]; metal-binding site 998088002085 pantoate--beta-alanine ligase; Region: panC; TIGR00018 998088002086 Pantoate-beta-alanine ligase; Region: PanC; cd00560 998088002087 active site 998088002088 ATP-binding site [chemical binding]; other site 998088002089 pantoate-binding site; other site 998088002090 HXXH motif; other site 998088002091 Uncharacterized conserved protein [Function unknown]; Region: COG1359 998088002092 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088002093 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 998088002094 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 998088002095 active site residue [active] 998088002096 exonuclease subunit SbcC; Provisional; Region: PRK10246 998088002097 inner membrane transport permease; Provisional; Region: PRK15066 998088002098 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 998088002099 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 998088002100 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 998088002101 Walker A/P-loop; other site 998088002102 ATP binding site [chemical binding]; other site 998088002103 Q-loop/lid; other site 998088002104 ABC transporter signature motif; other site 998088002105 Walker B; other site 998088002106 D-loop; other site 998088002107 H-loop/switch region; other site 998088002108 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 998088002109 active site 998088002110 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088002111 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088002112 aromatic acid decarboxylase; Validated; Region: PRK05920 998088002113 Flavoprotein; Region: Flavoprotein; pfam02441 998088002114 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 998088002115 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 998088002116 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 998088002117 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088002118 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 998088002119 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 998088002120 active site 998088002121 UDP-glucose 4-epimerase; Region: PLN02240 998088002122 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 998088002123 NAD binding site [chemical binding]; other site 998088002124 homodimer interface [polypeptide binding]; other site 998088002125 active site 998088002126 substrate binding site [chemical binding]; other site 998088002127 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 998088002128 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 998088002129 FAD binding pocket [chemical binding]; other site 998088002130 FAD binding motif [chemical binding]; other site 998088002131 phosphate binding motif [ion binding]; other site 998088002132 beta-alpha-beta structure motif; other site 998088002133 NAD binding pocket [chemical binding]; other site 998088002134 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 998088002135 catalytic loop [active] 998088002136 iron binding site [ion binding]; other site 998088002137 hybrid cluster protein; Provisional; Region: PRK05290 998088002138 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 998088002139 ACS interaction site; other site 998088002140 CODH interaction site; other site 998088002141 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 998088002142 hybrid metal cluster; other site 998088002143 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 998088002144 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 998088002145 dimerization interface [polypeptide binding]; other site 998088002146 DPS ferroxidase diiron center [ion binding]; other site 998088002147 ion pore; other site 998088002148 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 998088002149 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 998088002150 amidase catalytic site [active] 998088002151 Zn binding residues [ion binding]; other site 998088002152 substrate binding site [chemical binding]; other site 998088002153 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 998088002154 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 998088002155 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 998088002156 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 998088002157 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 998088002158 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 998088002159 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 998088002160 dimerization interface [polypeptide binding]; other site 998088002161 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 998088002162 dimer interface [polypeptide binding]; other site 998088002163 phosphorylation site [posttranslational modification] 998088002164 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 998088002165 ATP binding site [chemical binding]; other site 998088002166 Mg2+ binding site [ion binding]; other site 998088002167 G-X-G motif; other site 998088002168 Uncharacterized domain of BarA-like signal transduction histidine kinases [Signal transduction mechanisms]; Region: COG4999 998088002169 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 998088002170 active site 998088002171 phosphorylation site [posttranslational modification] 998088002172 intermolecular recognition site; other site 998088002173 dimerization interface [polypeptide binding]; other site 998088002174 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 998088002175 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 998088002176 TRAM domain; Region: TRAM; pfam01938 998088002177 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 998088002178 S-adenosylmethionine binding site [chemical binding]; other site 998088002179 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 998088002180 HD domain; Region: HD_4; pfam13328 998088002181 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 998088002182 synthetase active site [active] 998088002183 NTP binding site [chemical binding]; other site 998088002184 metal binding site [ion binding]; metal-binding site 998088002185 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 998088002186 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 998088002187 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 998088002188 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 998088002189 homodimer interface [polypeptide binding]; other site 998088002190 metal binding site [ion binding]; metal-binding site 998088002191 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 998088002192 homodimer interface [polypeptide binding]; other site 998088002193 active site 998088002194 putative chemical substrate binding site [chemical binding]; other site 998088002195 metal binding site [ion binding]; metal-binding site 998088002196 CTP synthetase; Validated; Region: pyrG; PRK05380 998088002197 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 998088002198 Catalytic site [active] 998088002199 active site 998088002200 UTP binding site [chemical binding]; other site 998088002201 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 998088002202 active site 998088002203 putative oxyanion hole; other site 998088002204 catalytic triad [active] 998088002205 enolase; Provisional; Region: eno; PRK00077 998088002206 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 998088002207 dimer interface [polypeptide binding]; other site 998088002208 metal binding site [ion binding]; metal-binding site 998088002209 substrate binding pocket [chemical binding]; other site 998088002210 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088002211 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 998088002212 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 998088002213 Coenzyme A binding pocket [chemical binding]; other site 998088002214 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 998088002215 binding surface 998088002216 TPR motif; other site 998088002217 Tetratricopeptide repeat; Region: TPR_12; pfam13424 998088002218 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 998088002219 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 998088002220 catalytic motif [active] 998088002221 Catalytic residue [active] 998088002222 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 998088002223 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 998088002224 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 998088002225 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 998088002226 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 998088002227 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 998088002228 Protein of unknown function (DUF2390); Region: DUF2390; pfam09523 998088002229 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 998088002230 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088002231 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088002232 ABC transporter; Region: ABC_tran_2; pfam12848 998088002233 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088002234 FOG: CBS domain [General function prediction only]; Region: COG0517 998088002235 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 998088002236 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 998088002237 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088002238 DNA-binding site [nucleotide binding]; DNA binding site 998088002239 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 998088002240 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088002241 homodimer interface [polypeptide binding]; other site 998088002242 catalytic residue [active] 998088002243 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 998088002244 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 998088002245 Aspartate racemase [Cell envelope biogenesis, outer membrane]; Region: RacX; COG1794 998088002246 aspartate racemase; Region: asp_race; TIGR00035 998088002247 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 998088002248 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 998088002249 putative acyl-acceptor binding pocket; other site 998088002250 Domain of unknown function (DUF386); Region: DUF386; cl01047 998088002251 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 998088002252 propionate/acetate kinase; Provisional; Region: PRK12379 998088002253 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 998088002254 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088002255 L,D-transpeptidase; Provisional; Region: PRK10190 998088002256 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 998088002257 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088002258 Protein of unknown function (DUF535); Region: DUF535; cl01128 998088002259 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 998088002260 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 998088002261 Na binding site [ion binding]; other site 998088002262 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 998088002263 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 998088002264 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 998088002265 substrate binding site; other site 998088002266 dimer interface; other site 998088002267 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 998088002268 homotrimer interaction site [polypeptide binding]; other site 998088002269 zinc binding site [ion binding]; other site 998088002270 CDP-binding sites; other site 998088002271 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 998088002272 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 998088002273 Permutation of conserved domain; other site 998088002274 active site 998088002275 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 998088002276 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 998088002277 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 998088002278 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 998088002279 S-adenosylmethionine binding site [chemical binding]; other site 998088002280 Predicted membrane protein [Function unknown]; Region: COG1238 998088002281 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 998088002282 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088002283 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088002284 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088002285 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 998088002286 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 998088002287 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088002288 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 998088002289 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 998088002290 DNA binding residues [nucleotide binding] 998088002291 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 998088002292 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 998088002293 FMN binding site [chemical binding]; other site 998088002294 active site 998088002295 substrate binding site [chemical binding]; other site 998088002296 catalytic residue [active] 998088002297 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088002298 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088002299 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002300 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088002301 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 998088002302 substrate binding pocket [chemical binding]; other site 998088002303 dimerization interface [polypeptide binding]; other site 998088002304 agmatine deiminase; Provisional; Region: PRK13551 998088002305 agmatine deiminase; Region: agmatine_aguA; TIGR03380 998088002306 amidase; Validated; Region: PRK06565 998088002307 Amidase; Region: Amidase; cl11426 998088002308 Amidase; Region: Amidase; cl11426 998088002309 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 998088002310 Polysaccharide biosynthesis protein; Region: Polysacc_synt_3; pfam13440 998088002311 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 998088002312 helicase 45; Provisional; Region: PTZ00424 998088002313 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 998088002314 ATP binding site [chemical binding]; other site 998088002315 Mg++ binding site [ion binding]; other site 998088002316 motif III; other site 998088002317 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 998088002318 nucleotide binding region [chemical binding]; other site 998088002319 ATP-binding site [chemical binding]; other site 998088002320 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088002321 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002322 metal binding site [ion binding]; metal-binding site 998088002323 active site 998088002324 I-site; other site 998088002325 Uncharacterized conserved protein [Function unknown]; Region: COG1912 998088002326 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 998088002327 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 998088002328 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 998088002329 Gamma carbonic anhydrases (CA): Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed...; Region: LbH_gamma_CA; cd00710 998088002330 trimer interface [polypeptide binding]; other site 998088002331 active site 998088002332 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2; cl00208 998088002333 CAS motifs; other site 998088002334 active site 998088002335 Nitronate monooxygenase; Region: NMO; pfam03060 998088002336 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 998088002337 FMN binding site [chemical binding]; other site 998088002338 substrate binding site [chemical binding]; other site 998088002339 putative catalytic residue [active] 998088002340 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_22; cd04681 998088002341 nudix motif; other site 998088002342 AsmA family; Region: AsmA; pfam05170 998088002343 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 998088002344 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 998088002345 Domain of unknown function (DUF3404); Region: DUF3404; pfam11884 998088002346 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088002347 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 998088002348 dimer interface [polypeptide binding]; other site 998088002349 phosphorylation site [posttranslational modification] 998088002350 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088002351 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 998088002352 active site 998088002353 phosphorylation site [posttranslational modification] 998088002354 intermolecular recognition site; other site 998088002355 dimerization interface [polypeptide binding]; other site 998088002356 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 998088002357 DNA binding site [nucleotide binding] 998088002358 Protein of unknown function (DUF2861); Region: DUF2861; pfam11060 998088002359 Glycosyl hydrolases related to GH101 family; Region: GHL; pfam11308 998088002360 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088002361 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 998088002362 Coenzyme A binding pocket [chemical binding]; other site 998088002363 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 998088002364 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 998088002365 metal binding triad; other site 998088002366 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 998088002367 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 998088002368 metal binding triad; other site 998088002369 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 998088002370 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088002371 Coenzyme A binding pocket [chemical binding]; other site 998088002372 HAMP domain; Region: HAMP; pfam00672 998088002373 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088002374 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088002375 dimer interface [polypeptide binding]; other site 998088002376 putative CheW interface [polypeptide binding]; other site 998088002377 Ion channel; Region: Ion_trans_2; pfam07885 998088002378 Bacterial SH3 domain homologues; Region: SH3b; smart00287 998088002379 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 998088002380 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 998088002381 Proline dehydrogenase; Region: Pro_dh; pfam01619 998088002382 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 998088002383 Glutamate binding site [chemical binding]; other site 998088002384 NAD binding site [chemical binding]; other site 998088002385 catalytic residues [active] 998088002386 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 998088002387 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 998088002388 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 998088002389 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 998088002390 putative NADH binding site [chemical binding]; other site 998088002391 putative active site [active] 998088002392 nudix motif; other site 998088002393 putative metal binding site [ion binding]; other site 998088002394 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 998088002395 substrate binding site [chemical binding]; other site 998088002396 active site 998088002397 fructokinase; Reviewed; Region: PRK09557 998088002398 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 998088002399 nucleotide binding site [chemical binding]; other site 998088002400 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 998088002401 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 998088002402 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 998088002403 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 998088002404 Phosphoglycerate kinase; Region: PGK; pfam00162 998088002405 substrate binding site [chemical binding]; other site 998088002406 hinge regions; other site 998088002407 ADP binding site [chemical binding]; other site 998088002408 catalytic site [active] 998088002409 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 998088002410 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 998088002411 active site 998088002412 intersubunit interface [polypeptide binding]; other site 998088002413 zinc binding site [ion binding]; other site 998088002414 Na+ binding site [ion binding]; other site 998088002415 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 998088002416 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088002417 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088002418 Coenzyme A binding pocket [chemical binding]; other site 998088002419 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 998088002420 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 998088002421 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 998088002422 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 998088002423 DsbD alpha interface [polypeptide binding]; other site 998088002424 catalytic residues [active] 998088002425 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 998088002426 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 998088002427 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 998088002428 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002429 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088002430 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 998088002431 dimerization interface [polypeptide binding]; other site 998088002432 putative global regulator; Reviewed; Region: PRK09559 998088002433 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 998088002434 Uncharacterized conserved protein [Function unknown]; Region: COG2938 998088002435 L-aspartate oxidase; Provisional; Region: PRK09077 998088002436 L-aspartate oxidase; Provisional; Region: PRK06175 998088002437 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 998088002438 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 998088002439 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088002440 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 998088002441 DNA binding residues [nucleotide binding] 998088002442 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 998088002443 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 998088002444 anti-sigma E factor; Provisional; Region: rseB; PRK09455 998088002445 MucB/RseB family; Region: MucB_RseB; pfam03888 998088002446 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 998088002447 GTP-binding protein LepA; Provisional; Region: PRK05433 998088002448 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 998088002449 G1 box; other site 998088002450 putative GEF interaction site [polypeptide binding]; other site 998088002451 GTP/Mg2+ binding site [chemical binding]; other site 998088002452 Switch I region; other site 998088002453 G2 box; other site 998088002454 G3 box; other site 998088002455 Switch II region; other site 998088002456 G4 box; other site 998088002457 G5 box; other site 998088002458 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 998088002459 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 998088002460 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 998088002461 signal peptidase I; Provisional; Region: PRK10861 998088002462 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 998088002463 Catalytic site [active] 998088002464 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 998088002465 ribonuclease III; Reviewed; Region: rnc; PRK00102 998088002466 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 998088002467 dimerization interface [polypeptide binding]; other site 998088002468 active site 998088002469 metal binding site [ion binding]; metal-binding site 998088002470 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 998088002471 dsRNA binding site [nucleotide binding]; other site 998088002472 GTPase Era; Reviewed; Region: era; PRK00089 998088002473 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 998088002474 G1 box; other site 998088002475 GTP/Mg2+ binding site [chemical binding]; other site 998088002476 Switch I region; other site 998088002477 G2 box; other site 998088002478 Switch II region; other site 998088002479 G3 box; other site 998088002480 G4 box; other site 998088002481 G5 box; other site 998088002482 KH domain; Region: KH_2; pfam07650 998088002483 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 998088002484 Recombination protein O N terminal; Region: RecO_N; pfam11967 998088002485 Recombination protein O C terminal; Region: RecO_C; pfam02565 998088002486 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 998088002487 active site 998088002488 hydrophilic channel; other site 998088002489 dimerization interface [polypeptide binding]; other site 998088002490 catalytic residues [active] 998088002491 active site lid [active] 998088002492 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 998088002493 intersubunit interface [polypeptide binding]; other site 998088002494 active site 998088002495 zinc binding site [ion binding]; other site 998088002496 Na+ binding site [ion binding]; other site 998088002497 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 998088002498 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 998088002499 active site 998088002500 dimer interface [polypeptide binding]; other site 998088002501 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; cd00006 998088002502 active pocket/dimerization site; other site 998088002503 active site 998088002504 phosphorylation site [posttranslational modification] 998088002505 Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]; Region: ManZ; COG3716 998088002506 Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIC [Carbohydrate transport and metabolism]; Region: ManY; COG3715 998088002507 PTS_IIB, PTS system, Mannose/sorbose specific IIB 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_IIB_man; cd00001 998088002508 active site 998088002509 phosphorylation site [posttranslational modification] 998088002510 putative sugar isomerase, AgaS family; Region: agaS_fam; TIGR02815 998088002511 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 998088002512 dimer interface [polypeptide binding]; other site 998088002513 active site 998088002514 AgaS-like protein. AgaS contains a SIS (Sugar ISomerase) domain which is found in many phosphosugar isomerases and phosphosugar binding proteins. AgaS is a putative isomerase in Escherichia coli. It is similar to the glucosamine-6-phosphate synthases; Region: SIS_AgaS_like; cd05010 998088002515 putative active site [active] 998088002516 Tagatose 6 phosphate kinase; Region: Tagatose_6_P_K; cl09211 998088002517 DNA-binding transcriptional regulator AgaR; Provisional; Region: PRK09802 998088002518 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 998088002519 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 998088002520 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 998088002521 active site 998088002522 YciI-like protein; Reviewed; Region: PRK11370 998088002523 intracellular septation protein A; Reviewed; Region: PRK00259 998088002524 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 998088002525 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088002526 catalytic residue [active] 998088002527 hemolysin; Provisional; Region: PRK15087 998088002528 putative transporter; Validated; Region: PRK03818 998088002529 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 998088002530 TrkA-C domain; Region: TrkA_C; pfam02080 998088002531 TrkA-C domain; Region: TrkA_C; pfam02080 998088002532 AspT/YidE/YbjL antiporter duplication domain; Region: YidE_YbjL_dupl; TIGR01625 998088002533 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 998088002534 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 998088002535 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 998088002536 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088002537 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; cd00198 998088002538 metal ion-dependent adhesion site (MIDAS); other site 998088002539 PAS fold; Region: PAS_4; pfam08448 998088002540 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 998088002541 putative active site [active] 998088002542 heme pocket [chemical binding]; other site 998088002543 PAS fold; Region: PAS_4; pfam08448 998088002544 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 998088002545 putative active site [active] 998088002546 heme pocket [chemical binding]; other site 998088002547 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088002548 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002549 metal binding site [ion binding]; metal-binding site 998088002550 active site 998088002551 I-site; other site 998088002552 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 998088002553 RNase E inhibitor protein; Provisional; Region: PRK11191 998088002554 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 998088002555 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 998088002556 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 998088002557 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 998088002558 active site 998088002559 zinc binding site [ion binding]; other site 998088002560 Indigoidine synthase A like protein; Region: Indigoidine_A; pfam04227 998088002561 putative kinase; Provisional; Region: PRK09954 998088002562 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 998088002563 putative DNA binding site [nucleotide binding]; other site 998088002564 putative Zn2+ binding site [ion binding]; other site 998088002565 YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; Region: YeiC_kinase_like; cd01941 998088002566 substrate binding site [chemical binding]; other site 998088002567 ATP binding site [chemical binding]; other site 998088002568 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 998088002569 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 998088002570 Ligand Binding Site [chemical binding]; other site 998088002571 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 998088002572 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 998088002573 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 998088002574 trimer interface [polypeptide binding]; other site 998088002575 eyelet of channel; other site 998088002576 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 998088002577 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 998088002578 S-adenosylmethionine binding site [chemical binding]; other site 998088002579 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 998088002580 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 998088002581 ligand binding site [chemical binding]; other site 998088002582 flexible hinge region; other site 998088002583 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 998088002584 putative switch regulator; other site 998088002585 non-specific DNA interactions [nucleotide binding]; other site 998088002586 DNA binding site [nucleotide binding] 998088002587 sequence specific DNA binding site [nucleotide binding]; other site 998088002588 putative cAMP binding site [chemical binding]; other site 998088002589 OsmC-like protein; Region: OsmC; cl00767 998088002590 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 998088002591 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 998088002592 phosphoribulokinase; Provisional; Region: PRK15453 998088002593 active site 998088002594 hypothetical protein; Provisional; Region: PRK04966 998088002595 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088002596 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002597 metal binding site [ion binding]; metal-binding site 998088002598 active site 998088002599 I-site; other site 998088002600 putative hydrolase; Provisional; Region: PRK10985 998088002601 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 998088002602 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088002603 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 998088002604 active site 998088002605 phosphorylation site [posttranslational modification] 998088002606 intermolecular recognition site; other site 998088002607 dimerization interface [polypeptide binding]; other site 998088002608 Probable metal-binding protein (DUF2387); Region: DUF2387; pfam09526 998088002609 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 998088002610 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 998088002611 Tim44-like domain; Region: Tim44; pfam04280 998088002612 replicative DNA helicase; Provisional; Region: PRK08840 998088002613 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 998088002614 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 998088002615 Walker A motif; other site 998088002616 ATP binding site [chemical binding]; other site 998088002617 Walker B motif; other site 998088002618 DNA binding loops [nucleotide binding] 998088002619 alanine racemase; Reviewed; Region: alr; PRK00053 998088002620 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 998088002621 active site 998088002622 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088002623 substrate binding site [chemical binding]; other site 998088002624 catalytic residues [active] 998088002625 dimer interface [polypeptide binding]; other site 998088002626 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 998088002627 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 998088002628 active site pocket [active] 998088002629 oxyanion hole [active] 998088002630 catalytic triad [active] 998088002631 active site nucleophile [active] 998088002632 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 998088002633 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 998088002634 Walker A/P-loop; other site 998088002635 ATP binding site [chemical binding]; other site 998088002636 Q-loop/lid; other site 998088002637 ABC transporter signature motif; other site 998088002638 Walker B; other site 998088002639 D-loop; other site 998088002640 H-loop/switch region; other site 998088002641 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 998088002642 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 998088002643 ABC-ATPase subunit interface; other site 998088002644 dimer interface [polypeptide binding]; other site 998088002645 putative PBP binding regions; other site 998088002646 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 998088002647 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 998088002648 intersubunit interface [polypeptide binding]; other site 998088002649 putative heme utilization carrier protein HutX; Region: HutX; TIGR04108 998088002650 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 998088002651 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 998088002652 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 998088002653 Isochorismatase family; Region: Isochorismatase; pfam00857 998088002654 catalytic triad [active] 998088002655 conserved cis-peptide bond; other site 998088002656 Protein of unknown function, DUF399; Region: DUF399; pfam04187 998088002657 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 998088002658 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 998088002659 N-terminal plug; other site 998088002660 ligand-binding site [chemical binding]; other site 998088002661 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 998088002662 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 998088002663 Zn binding site [ion binding]; other site 998088002664 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 998088002665 non-specific DNA binding site [nucleotide binding]; other site 998088002666 salt bridge; other site 998088002667 sequence-specific DNA binding site [nucleotide binding]; other site 998088002668 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 998088002669 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 998088002670 Na binding site [ion binding]; other site 998088002671 PAS domain; Region: PAS; smart00091 998088002672 PAS fold; Region: PAS_7; pfam12860 998088002673 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088002674 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 998088002675 dimer interface [polypeptide binding]; other site 998088002676 phosphorylation site [posttranslational modification] 998088002677 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 998088002678 ATP binding site [chemical binding]; other site 998088002679 Mg2+ binding site [ion binding]; other site 998088002680 G-X-G motif; other site 998088002681 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088002682 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 998088002683 active site 998088002684 phosphorylation site [posttranslational modification] 998088002685 intermolecular recognition site; other site 998088002686 dimerization interface [polypeptide binding]; other site 998088002687 N-terminal Early set domain associated with the catalytic domain of chitinase; Region: E_set_Chitinase_N; cd02848 998088002688 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 998088002689 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an...; Region: GH18_chitinase; cd06548 998088002690 active site 998088002691 PKD domain; Region: PKD; pfam00801 998088002692 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088002693 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002694 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088002695 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002696 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 998088002697 GAF domain; Region: GAF; pfam01590 998088002698 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088002699 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002700 metal binding site [ion binding]; metal-binding site 998088002701 active site 998088002702 I-site; other site 998088002703 N-terminal Early set domain associated with the catalytic domain of chitinase; Region: E_set_Chitinase_N; cd02848 998088002704 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 998088002705 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an...; Region: GH18_chitinase; cd06548 998088002706 active site 998088002707 REJ domain; Region: REJ; pfam02010 998088002708 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088002709 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002710 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088002711 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002712 Peptidase M66; Region: Peptidase_M66; pfam10462 998088002713 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088002714 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002715 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088002716 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002717 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088002718 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002719 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 998088002720 Glycoside hydrolase family 19 chitinase domain. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Family 19 chitinases are found primarily in plants (classes I, III, and IV), but some...; Region: chitinase_glyco_hydro_19; cd00325 998088002721 putative sugar binding site [chemical binding]; other site 998088002722 catalytic residues [active] 998088002723 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 998088002724 Chitin/cellulose binding domains of chitinase and related enzymes; Region: ChtBD3; cl00046 998088002725 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 998088002726 generic binding surface II; other site 998088002727 generic binding surface I; other site 998088002728 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 998088002729 putative catalytic site [active] 998088002730 putative metal binding site [ion binding]; other site 998088002731 putative phosphate binding site [ion binding]; other site 998088002732 Chitin/cellulose binding domains of chitinase and related enzymes; Region: ChtBD3; cl00046 998088002733 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002734 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 998088002735 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 998088002736 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an...; Region: GH18_chitinase; cd06548 998088002737 active site 998088002738 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 998088002739 Chitinase C; Region: ChiC; pfam06483 998088002740 Cellulose-binding domain, chitinase and related proteins; Region: CBD_like; cd12204 998088002741 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088002742 ligand binding site [chemical binding]; other site 998088002743 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 998088002744 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088002745 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 998088002746 active site 998088002747 phosphorylation site [posttranslational modification] 998088002748 intermolecular recognition site; other site 998088002749 dimerization interface [polypeptide binding]; other site 998088002750 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 998088002751 active site 998088002752 catalytic triad [active] 998088002753 oxyanion hole [active] 998088002754 switch loop; other site 998088002755 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 998088002756 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 998088002757 Walker A/P-loop; other site 998088002758 ATP binding site [chemical binding]; other site 998088002759 Q-loop/lid; other site 998088002760 ABC transporter signature motif; other site 998088002761 Walker B; other site 998088002762 D-loop; other site 998088002763 H-loop/switch region; other site 998088002764 FtsX-like permease family; Region: FtsX; pfam02687 998088002765 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 998088002766 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 998088002767 putative NAD(P) binding site [chemical binding]; other site 998088002768 putative active site [active] 998088002769 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 998088002770 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 998088002771 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 998088002772 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 998088002773 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 998088002774 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088002775 homodimer interface [polypeptide binding]; other site 998088002776 catalytic residue [active] 998088002777 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 998088002778 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 998088002779 S-adenosylmethionine binding site [chemical binding]; other site 998088002780 hypothetical protein; Provisional; Region: PRK11702 998088002781 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 998088002782 glutaminase; Provisional; Region: PRK00971 998088002783 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 998088002784 active site residue [active] 998088002785 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 998088002786 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 998088002787 active site residue [active] 998088002788 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 998088002789 active site residue [active] 998088002790 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 998088002791 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 998088002792 Protein of unknown function (DUF2541); Region: DUF2541; cl08090 998088002793 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 998088002794 MPT binding site; other site 998088002795 trimer interface [polypeptide binding]; other site 998088002796 Protein of unknown function (DUF3135); Region: DUF3135; pfam11333 998088002797 Uncharacterized conserved protein [Function unknown]; Region: COG2966 998088002798 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 998088002799 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 998088002800 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 998088002801 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 998088002802 folate binding site [chemical binding]; other site 998088002803 NADP+ binding site [chemical binding]; other site 998088002804 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 998088002805 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 998088002806 Active Sites [active] 998088002807 sulfite reductase subunit beta; Provisional; Region: PRK13504 998088002808 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 998088002809 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 998088002810 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 998088002811 Flavodoxin; Region: Flavodoxin_1; pfam00258 998088002812 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 998088002813 FAD binding pocket [chemical binding]; other site 998088002814 FAD binding motif [chemical binding]; other site 998088002815 catalytic residues [active] 998088002816 NAD binding pocket [chemical binding]; other site 998088002817 phosphate binding motif [ion binding]; other site 998088002818 beta-alpha-beta structure motif; other site 998088002819 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 998088002820 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 998088002821 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 998088002822 dimer interface [polypeptide binding]; other site 998088002823 putative anticodon binding site; other site 998088002824 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 998088002825 motif 1; other site 998088002826 active site 998088002827 motif 2; other site 998088002828 motif 3; other site 998088002829 peptide chain release factor 2; Provisional; Region: PRK08787 998088002830 This domain is found in peptide chain release factors; Region: PCRF; smart00937 998088002831 RF-1 domain; Region: RF-1; pfam00472 998088002832 Cache domain; Region: Cache_1; pfam02743 998088002833 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 998088002834 dimerization interface [polypeptide binding]; other site 998088002835 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088002836 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088002837 dimer interface [polypeptide binding]; other site 998088002838 putative CheW interface [polypeptide binding]; other site 998088002839 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 998088002840 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 998088002841 active site 998088002842 homodimer interface [polypeptide binding]; other site 998088002843 Protein of unknown function (DUF1315); Region: DUF1315; pfam07023 998088002844 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 998088002845 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 998088002846 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 998088002847 Protein of unknown function (DUF2989); Region: DUF2989; pfam11207 998088002848 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 998088002849 nudix motif; other site 998088002850 lipoyl synthase; Provisional; Region: PRK05481 998088002851 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 998088002852 FeS/SAM binding site; other site 998088002853 lipoate-protein ligase B; Provisional; Region: PRK14342 998088002854 hypothetical protein; Provisional; Region: PRK04998 998088002855 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 998088002856 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 998088002857 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 998088002858 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 998088002859 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 998088002860 Sporulation related domain; Region: SPOR; pfam05036 998088002861 Transglycosylase SLT domain; Region: SLT_2; pfam13406 998088002862 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 998088002863 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088002864 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 998088002865 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 998088002866 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 998088002867 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 998088002868 rRNA large subunit m3Psi methyltransferase RlmH; Region: tRNA_RlmH_YbeA; TIGR00246 998088002869 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 998088002870 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 998088002871 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 998088002872 active site 998088002873 (T/H)XGH motif; other site 998088002874 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 998088002875 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 998088002876 Lipopolysaccharide-assembly; Region: LptE; cl01125 998088002877 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 998088002878 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 998088002879 HIGH motif; other site 998088002880 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 998088002881 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 998088002882 active site 998088002883 KMSKS motif; other site 998088002884 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 998088002885 tRNA binding surface [nucleotide binding]; other site 998088002886 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 998088002887 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 998088002888 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 998088002889 flavodoxin FldB; Provisional; Region: PRK12359 998088002890 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 998088002891 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 998088002892 active site 998088002893 Int/Topo IB signature motif; other site 998088002894 Cache domain; Region: Cache_1; pfam02743 998088002895 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088002896 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002897 metal binding site [ion binding]; metal-binding site 998088002898 active site 998088002899 I-site; other site 998088002900 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 998088002901 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 998088002902 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 998088002903 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 998088002904 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 998088002905 DHH family; Region: DHH; pfam01368 998088002906 DHHA1 domain; Region: DHHA1; pfam02272 998088002907 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 998088002908 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 998088002909 putative active site [active] 998088002910 catalytic triad [active] 998088002911 putative dimer interface [polypeptide binding]; other site 998088002912 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 998088002913 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 998088002914 Transporter associated domain; Region: CorC_HlyC; smart01091 998088002915 metal-binding heat shock protein; Provisional; Region: PRK00016 998088002916 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 998088002917 PhoH-like protein; Region: PhoH; pfam02562 998088002918 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 998088002919 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 998088002920 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 998088002921 FeS/SAM binding site; other site 998088002922 TRAM domain; Region: TRAM; pfam01938 998088002923 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 998088002924 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK08849 998088002925 Isochorismatase family; Region: Isochorismatase; pfam00857 998088002926 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 998088002927 catalytic triad [active] 998088002928 conserved cis-peptide bond; other site 998088002929 PAS domain S-box; Region: sensory_box; TIGR00229 998088002930 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088002931 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088002932 metal binding site [ion binding]; metal-binding site 998088002933 active site 998088002934 I-site; other site 998088002935 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088002936 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088002937 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 998088002938 dimerization interface [polypeptide binding]; other site 998088002939 substrate binding pocket [chemical binding]; other site 998088002940 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 998088002941 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 998088002942 active site 998088002943 motif I; other site 998088002944 motif II; other site 998088002945 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 998088002946 dimer interface [polypeptide binding]; other site 998088002947 FMN binding site [chemical binding]; other site 998088002948 glycerate dehydrogenase; Provisional; Region: PRK06487 998088002949 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 998088002950 putative ligand binding site [chemical binding]; other site 998088002951 putative NAD binding site [chemical binding]; other site 998088002952 catalytic site [active] 998088002953 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 998088002954 elongation factor P; Validated; Region: PRK00529 998088002955 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 998088002956 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 998088002957 RNA binding site [nucleotide binding]; other site 998088002958 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 998088002959 RNA binding site [nucleotide binding]; other site 998088002960 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 998088002961 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 998088002962 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05096 998088002963 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 998088002964 active site 998088002965 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 998088002966 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 998088002967 dimer interface [polypeptide binding]; other site 998088002968 phosphorylation site [posttranslational modification] 998088002969 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 998088002970 ATP binding site [chemical binding]; other site 998088002971 Mg2+ binding site [ion binding]; other site 998088002972 G-X-G motif; other site 998088002973 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 998088002974 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 998088002975 active site 998088002976 phosphorylation site [posttranslational modification] 998088002977 intermolecular recognition site; other site 998088002978 dimerization interface [polypeptide binding]; other site 998088002979 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 998088002980 DNA binding site [nucleotide binding] 998088002981 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 998088002982 binding surface 998088002983 TPR motif; other site 998088002984 short chain dehydrogenase; Provisional; Region: PRK09072 998088002985 classical (c) SDRs; Region: SDR_c; cd05233 998088002986 NAD(P) binding site [chemical binding]; other site 998088002987 active site 998088002988 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 998088002989 heme binding pocket [chemical binding]; other site 998088002990 heme ligand [chemical binding]; other site 998088002991 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 998088002992 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_3; cd05914 998088002993 acyl-activating enzyme (AAE) consensus motif; other site 998088002994 putative AMP binding site [chemical binding]; other site 998088002995 putative active site [active] 998088002996 putative CoA binding site [chemical binding]; other site 998088002997 Thermostable hemolysin; Region: T_hemolysin; pfam12261 998088002998 Methyltransferase domain; Region: Methyltransf_23; pfam13489 998088002999 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 998088003000 S-adenosylmethionine binding site [chemical binding]; other site 998088003001 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 998088003002 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088003003 ABC transporter transmembrane region; Region: ABC_membrane_3; pfam13748 998088003004 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 998088003005 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088003006 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088003007 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 998088003008 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 998088003009 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 998088003010 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003011 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 998088003012 substrate binding pocket [chemical binding]; other site 998088003013 membrane-bound complex binding site; other site 998088003014 hinge residues; other site 998088003015 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 998088003016 hypothetical protein; Provisional; Region: PRK07338 998088003017 metal binding site [ion binding]; metal-binding site 998088003018 dimer interface [polypeptide binding]; other site 998088003019 hypothetical protein; Provisional; Region: PRK10519 998088003020 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 998088003021 Nucleoside recognition; Region: Gate; pfam07670 998088003022 Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitD; cd00547 998088003023 Iron-sulfur protein interface; other site 998088003024 proximal quinone binding site [chemical binding]; other site 998088003025 C-subunit interface; other site 998088003026 distal quinone binding site; other site 998088003027 Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitC; cd00546 998088003028 D-subunit interface [polypeptide binding]; other site 998088003029 Iron-sulfur protein interface; other site 998088003030 proximal quinone binding site [chemical binding]; other site 998088003031 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 998088003032 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 998088003033 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 998088003034 L-aspartate oxidase; Provisional; Region: PRK06175 998088003035 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 998088003036 Cache domain; Region: Cache_1; pfam02743 998088003037 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088003038 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 998088003039 dimerization interface [polypeptide binding]; other site 998088003040 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088003041 dimer interface [polypeptide binding]; other site 998088003042 putative CheW interface [polypeptide binding]; other site 998088003043 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 998088003044 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 998088003045 active site 998088003046 catalytic site [active] 998088003047 metal binding site [ion binding]; metal-binding site 998088003048 putative mechanosensitive channel protein; Provisional; Region: PRK10929 998088003049 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 998088003050 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088003051 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 998088003052 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 998088003053 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 998088003054 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088003055 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088003056 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088003057 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 998088003058 putative effector binding pocket; other site 998088003059 dimerization interface [polypeptide binding]; other site 998088003060 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 998088003061 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 998088003062 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 998088003063 catalytic residues [active] 998088003064 CHASE3 domain; Region: CHASE3; cl05000 998088003065 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088003066 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088003067 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 998088003068 dimerization interface [polypeptide binding]; other site 998088003069 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088003070 dimer interface [polypeptide binding]; other site 998088003071 putative CheW interface [polypeptide binding]; other site 998088003072 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 998088003073 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088003074 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 998088003075 dimerization interface [polypeptide binding]; other site 998088003076 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 998088003077 Transglycosylase; Region: Transgly; pfam00912 998088003078 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 998088003079 Competence protein A; Region: Competence_A; pfam11104 998088003080 Cell division protein FtsA; Region: FtsA; cl17206 998088003081 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 998088003082 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 998088003083 Pilus assembly protein, PilO; Region: PilO; pfam04350 998088003084 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 998088003085 Pilus assembly protein, PilP; Region: PilP; pfam04351 998088003086 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 998088003087 Secretin and TonB N terminus short domain; Region: STN; smart00965 998088003088 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 998088003089 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 998088003090 shikimate kinase; Reviewed; Region: aroK; PRK00131 998088003091 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 998088003092 ADP binding site [chemical binding]; other site 998088003093 magnesium binding site [ion binding]; other site 998088003094 putative shikimate binding site; other site 998088003095 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 998088003096 active site 998088003097 dimer interface [polypeptide binding]; other site 998088003098 metal binding site [ion binding]; metal-binding site 998088003099 AAA domain; Region: AAA_22; pfam13401 998088003100 cell division protein DamX; Validated; Region: PRK10905 998088003101 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 998088003102 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 998088003103 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 998088003104 substrate binding site [chemical binding]; other site 998088003105 hexamer interface [polypeptide binding]; other site 998088003106 metal binding site [ion binding]; metal-binding site 998088003107 phosphoglycolate phosphatase; Provisional; Region: PRK13222 998088003108 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 998088003109 motif II; other site 998088003110 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 998088003111 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 998088003112 active site 998088003113 HIGH motif; other site 998088003114 dimer interface [polypeptide binding]; other site 998088003115 KMSKS motif; other site 998088003116 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 998088003117 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 998088003118 glutamine binding [chemical binding]; other site 998088003119 catalytic triad [active] 998088003120 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 998088003121 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 998088003122 inhibitor-cofactor binding pocket; inhibition site 998088003123 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088003124 catalytic residue [active] 998088003125 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 998088003126 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 998088003127 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 998088003128 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 998088003129 NAD(P) binding site [chemical binding]; other site 998088003130 catalytic residues [active] 998088003131 Domain of unknown function (DUF1338); Region: DUF1338; pfam07063 998088003132 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 998088003133 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 998088003134 active site 998088003135 motif I; other site 998088003136 motif II; other site 998088003137 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 998088003138 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 998088003139 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 998088003140 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 998088003141 dimer interface [polypeptide binding]; other site 998088003142 PYR/PP interface [polypeptide binding]; other site 998088003143 TPP binding site [chemical binding]; other site 998088003144 substrate binding site [chemical binding]; other site 998088003145 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 998088003146 Domain of unknown function; Region: EKR; pfam10371 998088003147 4Fe-4S binding domain; Region: Fer4_6; pfam12837 998088003148 4Fe-4S binding domain; Region: Fer4; pfam00037 998088003149 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 998088003150 TPP-binding site [chemical binding]; other site 998088003151 dimer interface [polypeptide binding]; other site 998088003152 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 998088003153 trehalose-6-phosphate hydrolase; Provisional; Region: PRK10933 998088003154 Ca binding site [ion binding]; other site 998088003155 active site 998088003156 catalytic site [active] 998088003157 Protein of unknown function (DUF1622); Region: DUF1622; pfam07784 998088003158 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 998088003159 ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as...; Region: ASCH_yqfb_like; cd06552 998088003160 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 998088003161 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 998088003162 ligand binding site [chemical binding]; other site 998088003163 flexible hinge region; other site 998088003164 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 998088003165 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 998088003166 nicotinamide riboside transporter PnuC; Provisional; Region: PRK15397 998088003167 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 998088003168 transmembrane helices; other site 998088003169 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 998088003170 TrkA-C domain; Region: TrkA_C; pfam02080 998088003171 TrkA-C domain; Region: TrkA_C; pfam02080 998088003172 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 998088003173 GTP-binding protein YchF; Reviewed; Region: PRK09601 998088003174 YchF GTPase; Region: YchF; cd01900 998088003175 G1 box; other site 998088003176 GTP/Mg2+ binding site [chemical binding]; other site 998088003177 Switch I region; other site 998088003178 G2 box; other site 998088003179 Switch II region; other site 998088003180 G3 box; other site 998088003181 G4 box; other site 998088003182 G5 box; other site 998088003183 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 998088003184 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 998088003185 putative active site [active] 998088003186 catalytic residue [active] 998088003187 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 998088003188 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 998088003189 active site 998088003190 metal binding site [ion binding]; metal-binding site 998088003191 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 998088003192 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 998088003193 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 998088003194 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 998088003195 active site 998088003196 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 998088003197 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 998088003198 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 998088003199 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 998088003200 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 998088003201 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 998088003202 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 998088003203 tRNA; other site 998088003204 putative tRNA binding site [nucleotide binding]; other site 998088003205 putative NADP binding site [chemical binding]; other site 998088003206 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 998088003207 peptide chain release factor 1; Validated; Region: prfA; PRK00591 998088003208 This domain is found in peptide chain release factors; Region: PCRF; smart00937 998088003209 RF-1 domain; Region: RF-1; pfam00472 998088003210 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 998088003211 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 998088003212 S-adenosylmethionine binding site [chemical binding]; other site 998088003213 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 998088003214 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 998088003215 Tetratricopeptide repeat; Region: TPR_9; pfam13371 998088003216 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 998088003217 TPR motif; other site 998088003218 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088003219 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 998088003220 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 998088003221 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 998088003222 autonomous glycyl radical cofactor GrcA; Region: spare_glycyl; TIGR04365 998088003223 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 998088003224 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003225 substrate binding pocket [chemical binding]; other site 998088003226 membrane-bound complex binding site; other site 998088003227 hinge residues; other site 998088003228 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 998088003229 ligand binding site [chemical binding]; other site 998088003230 active site 998088003231 UGI interface [polypeptide binding]; other site 998088003232 catalytic site [active] 998088003233 Hemerythrin-like domain; Region: Hr-like; cd12108 998088003234 Fe binding site [ion binding]; other site 998088003235 alpha-glucosidase; Provisional; Region: PRK10137 998088003236 Protein of unknown function, DUF608; Region: DUF608; pfam04685 998088003237 Trehalase; Region: Trehalase; cl17346 998088003238 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088003239 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088003240 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 998088003241 substrate binding site [chemical binding]; other site 998088003242 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 998088003243 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 998088003244 GDP-binding site [chemical binding]; other site 998088003245 ACT binding site; other site 998088003246 IMP binding site; other site 998088003247 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088003248 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088003249 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 998088003250 dimerization interface [polypeptide binding]; other site 998088003251 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 998088003252 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 998088003253 putative C-S lyase; Region: C_S_lyase_PatB; TIGR04350 998088003254 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 998088003255 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088003256 homodimer interface [polypeptide binding]; other site 998088003257 catalytic residue [active] 998088003258 sugar efflux transporter B; Provisional; Region: PRK15011 998088003259 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 998088003260 putative substrate translocation pore; other site 998088003261 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088003262 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088003263 dimerization interface [polypeptide binding]; other site 998088003264 LysR substrate binding domain; Region: LysR_substrate; pfam03466 998088003265 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 998088003266 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088003267 NAD(P) binding site [chemical binding]; other site 998088003268 active site 998088003269 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 998088003270 putative inner membrane peptidase; Provisional; Region: PRK11778 998088003271 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 998088003272 tandem repeat interface [polypeptide binding]; other site 998088003273 oligomer interface [polypeptide binding]; other site 998088003274 active site residues [active] 998088003275 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 998088003276 Major Facilitator Superfamily; Region: MFS_1; pfam07690 998088003277 Uncharacterized conserved protein involved in intracellular sulfur reduction [Inorganic ion transport and metabolism]; Region: DsrE; COG1553 998088003278 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 998088003279 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 998088003280 putative protease; Provisional; Region: PRK15452 998088003281 Peptidase family U32; Region: Peptidase_U32; pfam01136 998088003282 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 998088003283 putative fimbrial protein TcfA; Provisional; Region: PRK15308 998088003284 fimbrial outer membrane usher protein TcfC; Provisional; Region: PRK15310 998088003285 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 998088003286 transcriptional regulator RcsB; Provisional; Region: PRK10840 998088003287 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 998088003288 active site 998088003289 phosphorylation site [posttranslational modification] 998088003290 intermolecular recognition site; other site 998088003291 dimerization interface [polypeptide binding]; other site 998088003292 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 998088003293 DNA binding residues [nucleotide binding] 998088003294 dimerization interface [polypeptide binding]; other site 998088003295 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003296 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 998088003297 substrate binding pocket [chemical binding]; other site 998088003298 membrane-bound complex binding site; other site 998088003299 hinge residues; other site 998088003300 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 998088003301 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003302 substrate binding pocket [chemical binding]; other site 998088003303 membrane-bound complex binding site; other site 998088003304 hinge residues; other site 998088003305 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 998088003306 dimer interface [polypeptide binding]; other site 998088003307 phosphorylation site [posttranslational modification] 998088003308 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 998088003309 ATP binding site [chemical binding]; other site 998088003310 Mg2+ binding site [ion binding]; other site 998088003311 G-X-G motif; other site 998088003312 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003313 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 998088003314 active site 998088003315 phosphorylation site [posttranslational modification] 998088003316 intermolecular recognition site; other site 998088003317 dimerization interface [polypeptide binding]; other site 998088003318 succinylarginine dihydrolase; Provisional; Region: PRK13281 998088003319 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 998088003320 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 998088003321 active site 998088003322 interdomain interaction site; other site 998088003323 putative metal-binding site [ion binding]; other site 998088003324 nucleotide binding site [chemical binding]; other site 998088003325 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 998088003326 domain I; other site 998088003327 DNA binding groove [nucleotide binding] 998088003328 phosphate binding site [ion binding]; other site 998088003329 domain II; other site 998088003330 domain III; other site 998088003331 nucleotide binding site [chemical binding]; other site 998088003332 catalytic site [active] 998088003333 domain IV; other site 998088003334 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 998088003335 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 998088003336 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 998088003337 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 998088003338 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 998088003339 active site 998088003340 DNA binding site [nucleotide binding] 998088003341 PAS domain; Region: PAS_9; pfam13426 998088003342 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 998088003343 putative active site [active] 998088003344 heme pocket [chemical binding]; other site 998088003345 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088003346 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088003347 dimer interface [polypeptide binding]; other site 998088003348 putative CheW interface [polypeptide binding]; other site 998088003349 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 998088003350 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 998088003351 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 998088003352 active site 998088003353 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 998088003354 N-terminal Early set domain associated with the catalytic domain of cellulase; Region: E_set_Cellulase_N; cd02850 998088003355 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 998088003356 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088003357 Walker A/P-loop; other site 998088003358 ATP binding site [chemical binding]; other site 998088003359 Q-loop/lid; other site 998088003360 ABC transporter signature motif; other site 998088003361 Walker B; other site 998088003362 D-loop; other site 998088003363 H-loop/switch region; other site 998088003364 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 998088003365 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 998088003366 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088003367 Walker A/P-loop; other site 998088003368 ATP binding site [chemical binding]; other site 998088003369 Q-loop/lid; other site 998088003370 ABC transporter signature motif; other site 998088003371 Walker B; other site 998088003372 D-loop; other site 998088003373 H-loop/switch region; other site 998088003374 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088003375 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 998088003376 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 998088003377 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 998088003378 dimer interface [polypeptide binding]; other site 998088003379 conserved gate region; other site 998088003380 putative PBP binding loops; other site 998088003381 ABC-ATPase subunit interface; other site 998088003382 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 998088003383 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 998088003384 dimer interface [polypeptide binding]; other site 998088003385 conserved gate region; other site 998088003386 putative PBP binding loops; other site 998088003387 ABC-ATPase subunit interface; other site 998088003388 The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold; Region: PBP2_TmCBP_oligosaccharides_like; cd08509 998088003389 substrate binding site [chemical binding]; other site 998088003390 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 998088003391 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088003392 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 998088003393 dimerization interface [polypeptide binding]; other site 998088003394 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 998088003395 dimer interface [polypeptide binding]; other site 998088003396 phosphorylation site [posttranslational modification] 998088003397 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 998088003398 ATP binding site [chemical binding]; other site 998088003399 Mg2+ binding site [ion binding]; other site 998088003400 G-X-G motif; other site 998088003401 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 998088003402 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003403 active site 998088003404 phosphorylation site [posttranslational modification] 998088003405 intermolecular recognition site; other site 998088003406 dimerization interface [polypeptide binding]; other site 998088003407 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 998088003408 PAS fold; Region: PAS_4; pfam08448 998088003409 putative active site [active] 998088003410 heme pocket [chemical binding]; other site 998088003411 Protein of unknown function (DUF2517); Region: DUF2517; pfam10725 998088003412 Predicted integral membrane protein (DUF2282); Region: DUF2282; pfam10048 998088003413 hypothetical protein; Provisional; Region: PRK05409 998088003414 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 998088003415 Predicted membrane protein [Function unknown]; Region: COG2259 998088003416 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 998088003417 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088003418 Coenzyme A binding pocket [chemical binding]; other site 998088003419 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 998088003420 PAS domain; Region: PAS_9; pfam13426 998088003421 putative active site [active] 998088003422 heme pocket [chemical binding]; other site 998088003423 PAS domain; Region: PAS_9; pfam13426 998088003424 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 998088003425 putative active site [active] 998088003426 heme pocket [chemical binding]; other site 998088003427 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088003428 dimer interface [polypeptide binding]; other site 998088003429 putative CheW interface [polypeptide binding]; other site 998088003430 Domain of unknown function (DUF3332); Region: DUF3332; pfam11810 998088003431 Predicted membrane protein [Function unknown]; Region: COG1289 998088003432 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 998088003433 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional; Region: PRK14491 998088003434 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 998088003435 Walker A motif; other site 998088003436 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 998088003437 dimer interface [polypeptide binding]; other site 998088003438 putative functional site; other site 998088003439 putative MPT binding site; other site 998088003440 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 998088003441 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 998088003442 GTP binding site; other site 998088003443 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 998088003444 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 998088003445 Walker A/P-loop; other site 998088003446 ATP binding site [chemical binding]; other site 998088003447 Q-loop/lid; other site 998088003448 ABC transporter signature motif; other site 998088003449 Walker B; other site 998088003450 D-loop; other site 998088003451 H-loop/switch region; other site 998088003452 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 998088003453 dimer interface [polypeptide binding]; other site 998088003454 conserved gate region; other site 998088003455 putative PBP binding loops; other site 998088003456 ABC-ATPase subunit interface; other site 998088003457 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 998088003458 dimerization interface [polypeptide binding]; other site 998088003459 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 998088003460 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 998088003461 active site 998088003462 phosphorylation site [posttranslational modification] 998088003463 intermolecular recognition site; other site 998088003464 dimerization interface [polypeptide binding]; other site 998088003465 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 998088003466 Walker A motif; other site 998088003467 ATP binding site [chemical binding]; other site 998088003468 Walker B motif; other site 998088003469 arginine finger; other site 998088003470 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 998088003471 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 998088003472 dimer interface [polypeptide binding]; other site 998088003473 phosphorylation site [posttranslational modification] 998088003474 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 998088003475 ATP binding site [chemical binding]; other site 998088003476 G-X-G motif; other site 998088003477 Helix-turn-helix domain; Region: HTH_17; pfam12728 998088003478 PBP superfamily domain; Region: PBP_like; pfam12727 998088003479 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 998088003480 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 998088003481 Radical SAM superfamily; Region: Radical_SAM; pfam04055 998088003482 FeS/SAM binding site; other site 998088003483 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 998088003484 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 998088003485 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 998088003486 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 998088003487 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 998088003488 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 998088003489 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 998088003490 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 998088003491 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 998088003492 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 998088003493 [4Fe-4S] binding site [ion binding]; other site 998088003494 molybdopterin cofactor binding site; other site 998088003495 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 998088003496 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 998088003497 molybdopterin cofactor binding site; other site 998088003498 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 998088003499 4Fe-4S binding domain; Region: Fer4; cl02805 998088003500 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 998088003501 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 998088003502 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003503 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 998088003504 substrate binding pocket [chemical binding]; other site 998088003505 membrane-bound complex binding site; other site 998088003506 hinge residues; other site 998088003507 malate dehydrogenase; Provisional; Region: PRK13529 998088003508 Malic enzyme, N-terminal domain; Region: malic; pfam00390 998088003509 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 998088003510 NAD(P) binding site [chemical binding]; other site 998088003511 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 998088003512 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; cd00081 998088003513 protein-splicing catalytic site; other site 998088003514 thioester formation/cholesterol transfer; other site 998088003515 uracil-xanthine permease; Region: ncs2; TIGR00801 998088003516 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003517 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 998088003518 substrate binding pocket [chemical binding]; other site 998088003519 membrane-bound complex binding site; other site 998088003520 hinge residues; other site 998088003521 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 998088003522 dimerization interface [polypeptide binding]; other site 998088003523 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088003524 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088003525 dimer interface [polypeptide binding]; other site 998088003526 putative CheW interface [polypeptide binding]; other site 998088003527 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 998088003528 DNA binding site [nucleotide binding] 998088003529 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 998088003530 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088003531 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 998088003532 Coenzyme A binding pocket [chemical binding]; other site 998088003533 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 998088003534 putative hydrophobic ligand binding site [chemical binding]; other site 998088003535 glucokinase; Provisional; Region: glk; PRK00292 998088003536 glucokinase, proteobacterial type; Region: glk; TIGR00749 998088003537 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 998088003538 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 998088003539 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 998088003540 putative active site [active] 998088003541 pyruvate kinase; Provisional; Region: PRK05826 998088003542 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 998088003543 domain interfaces; other site 998088003544 active site 998088003545 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cl01109 998088003546 putative amphipathic alpha helix; other site 998088003547 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 998088003548 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 998088003549 active site 998088003550 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088003551 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088003552 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 998088003553 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 998088003554 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 998088003555 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 998088003556 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 998088003557 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 998088003558 MgtE intracellular N domain; Region: MgtE_N; smart00924 998088003559 FliG C-terminal domain; Region: FliG_C; pfam01706 998088003560 type III secretion apparatus protein, HrpE/YscL family; Region: HrpE_YscL_not; TIGR02499 998088003561 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 998088003562 Flagellar assembly protein FliH; Region: FliH; pfam02108 998088003563 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08972 998088003564 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 998088003565 Walker A motif/ATP binding site; other site 998088003566 Walker B motif; other site 998088003567 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 998088003568 Flagellar FliJ protein; Region: FliJ; pfam02050 998088003569 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 998088003570 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK05696 998088003571 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 998088003572 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 998088003573 flagellar motor switch protein; Validated; Region: fliN; PRK05698 998088003574 flagellar motor switch protein; Validated; Region: fliN; PRK08983 998088003575 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 998088003576 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 998088003577 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 998088003578 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 998088003579 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 998088003580 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 998088003581 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 998088003582 FHIPEP family; Region: FHIPEP; pfam00771 998088003583 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 998088003584 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 998088003585 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 998088003586 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 998088003587 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 998088003588 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 998088003589 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088003590 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 998088003591 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 998088003592 DNA binding residues [nucleotide binding] 998088003593 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 998088003594 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 998088003595 active site 998088003596 phosphorylation site [posttranslational modification] 998088003597 intermolecular recognition site; other site 998088003598 dimerization interface [polypeptide binding]; other site 998088003599 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 998088003600 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 998088003601 putative binding surface; other site 998088003602 active site 998088003603 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 998088003604 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 998088003605 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 998088003606 ATP binding site [chemical binding]; other site 998088003607 Mg2+ binding site [ion binding]; other site 998088003608 G-X-G motif; other site 998088003609 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 998088003610 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 998088003611 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 998088003612 active site 998088003613 phosphorylation site [posttranslational modification] 998088003614 intermolecular recognition site; other site 998088003615 dimerization interface [polypeptide binding]; other site 998088003616 CheB methylesterase; Region: CheB_methylest; pfam01339 998088003617 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088003618 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 998088003619 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 998088003620 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 998088003621 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088003622 ligand binding site [chemical binding]; other site 998088003623 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 998088003624 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 998088003625 P-loop; other site 998088003626 Magnesium ion binding site [ion binding]; other site 998088003627 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 998088003628 Magnesium ion binding site [ion binding]; other site 998088003629 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; cd00588 998088003630 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 998088003631 putative CheA interaction surface; other site 998088003632 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 998088003633 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 998088003634 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 998088003635 Cytochrome c biogenesis ATP-binding export protein; Region: ABC_CcmA_heme_exporter; cd03231 998088003636 Walker A/P-loop; other site 998088003637 ATP binding site [chemical binding]; other site 998088003638 Q-loop/lid; other site 998088003639 ABC transporter signature motif; other site 998088003640 Walker B; other site 998088003641 D-loop; other site 998088003642 H-loop/switch region; other site 998088003643 heme exporter protein CcmB; Region: ccmB; TIGR01190 998088003644 heme exporter protein CcmC; Region: ccmC; TIGR01191 998088003645 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 998088003646 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13165 998088003647 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 998088003648 thiol:disulfide interchange protein DsbE; Provisional; Region: PRK15412 998088003649 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 998088003650 catalytic residues [active] 998088003651 central insert; other site 998088003652 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 998088003653 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 998088003654 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 998088003655 VacJ like lipoprotein; Region: VacJ; cl01073 998088003656 superoxide dismutase; Provisional; Region: PRK10543 998088003657 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 998088003658 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 998088003659 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 998088003660 putative GSH binding site [chemical binding]; other site 998088003661 catalytic residues [active] 998088003662 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 998088003663 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 998088003664 tetramer interface [polypeptide binding]; other site 998088003665 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088003666 catalytic residue [active] 998088003667 threonine/serine transporter TdcC; Provisional; Region: PRK13629 998088003668 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088003669 propionate/acetate kinase; Provisional; Region: PRK12379 998088003670 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 998088003671 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 998088003672 Pyruvate formate lyase 1; Region: PFL1; cd01678 998088003673 coenzyme A binding site [chemical binding]; other site 998088003674 active site 998088003675 catalytic residues [active] 998088003676 glycine loop; other site 998088003677 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 998088003678 homotrimer interaction site [polypeptide binding]; other site 998088003679 putative active site [active] 998088003680 16S rRNA methyltransferase B; Provisional; Region: PRK14902 998088003681 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 998088003682 S-adenosylmethionine binding site [chemical binding]; other site 998088003683 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_2; pfam13574 998088003684 active site 998088003685 Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; Region: GPI-anchored; pfam10342 998088003686 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_2; pfam13574 998088003687 active site 998088003688 Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; Region: GPI-anchored; pfam10342 998088003689 Metallo-peptidase family M12B Reprolysin-like; Region: Reprolysin_2; pfam13574 998088003690 active site 998088003691 Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; Region: GPI-anchored; pfam10342 998088003692 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 998088003693 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 998088003694 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 998088003695 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 998088003696 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 998088003697 putative C-terminal domain interface [polypeptide binding]; other site 998088003698 putative GSH binding site (G-site) [chemical binding]; other site 998088003699 putative dimer interface [polypeptide binding]; other site 998088003700 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 998088003701 N-terminal domain interface [polypeptide binding]; other site 998088003702 dimer interface [polypeptide binding]; other site 998088003703 substrate binding pocket (H-site) [chemical binding]; other site 998088003704 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 998088003705 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088003706 Coenzyme A binding pocket [chemical binding]; other site 998088003707 Uncharacterized conserved protein [Function unknown]; Region: COG2850 998088003708 adenylosuccinate lyase; Provisional; Region: PRK09285 998088003709 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 998088003710 tetramer interface [polypeptide binding]; other site 998088003711 active site 998088003712 putative lysogenization regulator; Reviewed; Region: PRK00218 998088003713 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 998088003714 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 998088003715 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 998088003716 nudix motif; other site 998088003717 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 998088003718 pseudouridine synthase; Region: TIGR00093 998088003719 active site 998088003720 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 998088003721 regulatory protein interface [polypeptide binding]; other site 998088003722 active site 998088003723 regulatory phosphorylation site [posttranslational modification]; other site 998088003724 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 998088003725 active site 998088003726 phosphorylation site [posttranslational modification] 998088003727 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 998088003728 active site 998088003729 P-loop; other site 998088003730 phosphorylation site [posttranslational modification] 998088003731 sugar phosphate antiporter; Reviewed; Region: uhpT; PRK09556 998088003732 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 998088003733 putative substrate translocation pore; other site 998088003734 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 998088003735 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 998088003736 active site 998088003737 phosphorylation site [posttranslational modification] 998088003738 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 998088003739 active site 998088003740 P-loop; other site 998088003741 phosphorylation site [posttranslational modification] 998088003742 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; COG1299 998088003743 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 998088003744 Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes SLAC1 (Slow Anion Channel-Associated 1); Region: TDT_SLAC1_like; cd09323 998088003745 gating phenylalanine in ion channel; other site 998088003746 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 998088003747 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 998088003748 CoenzymeA binding site [chemical binding]; other site 998088003749 subunit interaction site [polypeptide binding]; other site 998088003750 PHB binding site; other site 998088003751 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 998088003752 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 998088003753 dimerization interface [polypeptide binding]; other site 998088003754 DPS ferroxidase diiron center [ion binding]; other site 998088003755 ion pore; other site 998088003756 Phosphotransferase enzyme family; Region: APH; pfam01636 998088003757 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 998088003758 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; cd02019 998088003759 active site 998088003760 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 998088003761 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 998088003762 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 998088003763 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088003764 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 998088003765 Coenzyme A binding pocket [chemical binding]; other site 998088003766 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088003767 Coenzyme A binding pocket [chemical binding]; other site 998088003768 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 998088003769 Dimer interface [polypeptide binding]; other site 998088003770 BRCT sequence motif; other site 998088003771 DNA-binding transcriptional repressor MalI; Provisional; Region: PRK10014 998088003772 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088003773 DNA binding site [nucleotide binding] 998088003774 domain linker motif; other site 998088003775 Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; Region: PBP1_MalI_like; cd06289 998088003776 putative dimerization interface [polypeptide binding]; other site 998088003777 putative ligand binding site [chemical binding]; other site 998088003778 bifunctional PTS system maltose and glucose-specific transporter subunits IICB; Provisional; Region: PRK10110 998088003779 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 998088003780 PTS_IIB, PTS system, glucose/sucrose specific IIB 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_IIB_glc; cd00212 998088003781 active site turn [active] 998088003782 phosphorylation site [posttranslational modification] 998088003783 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 998088003784 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 998088003785 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088003786 homodimer interface [polypeptide binding]; other site 998088003787 catalytic residue [active] 998088003788 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 998088003789 active site 998088003790 putative DNA-binding cleft [nucleotide binding]; other site 998088003791 dimer interface [polypeptide binding]; other site 998088003792 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088003793 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088003794 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 998088003795 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 998088003796 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 998088003797 active site 998088003798 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 998088003799 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088003800 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088003801 putative hydrolase; Validated; Region: PRK09248 998088003802 Polymerase and Histidinol Phosphatase domain of Ycdx like; Region: PHP_HisPPase_Ycdx_like; cd07437 998088003803 active site 998088003804 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 998088003805 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 998088003806 catalytic loop [active] 998088003807 iron binding site [ion binding]; other site 998088003808 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 998088003809 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088003810 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088003811 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 998088003812 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 998088003813 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 998088003814 [4Fe-4S] binding site [ion binding]; other site 998088003815 molybdopterin cofactor binding site; other site 998088003816 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_CT_Formate-Dh_H; cd02790 998088003817 molybdopterin cofactor binding site; other site 998088003818 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 998088003819 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003820 active site 998088003821 phosphorylation site [posttranslational modification] 998088003822 intermolecular recognition site; other site 998088003823 dimerization interface [polypeptide binding]; other site 998088003824 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 998088003825 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003826 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 998088003827 substrate binding pocket [chemical binding]; other site 998088003828 membrane-bound complex binding site; other site 998088003829 hinge residues; other site 998088003830 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 998088003831 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088003832 substrate binding pocket [chemical binding]; other site 998088003833 membrane-bound complex binding site; other site 998088003834 hinge residues; other site 998088003835 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 998088003836 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 998088003837 dimer interface [polypeptide binding]; other site 998088003838 phosphorylation site [posttranslational modification] 998088003839 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 998088003840 ATP binding site [chemical binding]; other site 998088003841 Mg2+ binding site [ion binding]; other site 998088003842 G-X-G motif; other site 998088003843 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003844 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 998088003845 active site 998088003846 phosphorylation site [posttranslational modification] 998088003847 intermolecular recognition site; other site 998088003848 dimerization interface [polypeptide binding]; other site 998088003849 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 998088003850 putative binding surface; other site 998088003851 active site 998088003852 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 998088003853 SmpB-tmRNA interface; other site 998088003854 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 998088003855 putative coenzyme Q binding site [chemical binding]; other site 998088003856 hypothetical protein; Validated; Region: PRK01777 998088003857 M20 Peptidases Aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase from bacteria and archaea; Region: M20_Acy1_IAAspH_bact; cd05665 998088003858 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 998088003859 putative metal binding site [ion binding]; other site 998088003860 dimer interface [polypeptide binding]; other site 998088003861 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 998088003862 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 998088003863 active site 998088003864 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 998088003865 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 998088003866 dimer interface [polypeptide binding]; other site 998088003867 active site 998088003868 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 998088003869 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 998088003870 putative active site [active] 998088003871 putative dimer interface [polypeptide binding]; other site 998088003872 Hpt domain; Region: Hpt; pfam01627 998088003873 putative binding surface; other site 998088003874 active site 998088003875 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 998088003876 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 998088003877 phosphate binding site [ion binding]; other site 998088003878 putative substrate binding pocket [chemical binding]; other site 998088003879 dimer interface [polypeptide binding]; other site 998088003880 Uncharacterized conserved protein [Function unknown]; Region: COG3287 998088003881 FIST N domain; Region: FIST; pfam08495 998088003882 FIST C domain; Region: FIST_C; pfam10442 998088003883 PAS domain; Region: PAS_9; pfam13426 998088003884 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088003885 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 998088003886 dimer interface [polypeptide binding]; other site 998088003887 phosphorylation site [posttranslational modification] 998088003888 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 998088003889 ATP binding site [chemical binding]; other site 998088003890 Mg2+ binding site [ion binding]; other site 998088003891 G-X-G motif; other site 998088003892 Response regulator receiver domain; Region: Response_reg; pfam00072 998088003893 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 998088003894 active site 998088003895 phosphorylation site [posttranslational modification] 998088003896 intermolecular recognition site; other site 998088003897 dimerization interface [polypeptide binding]; other site 998088003898 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 998088003899 transcriptional regulator NarL; Provisional; Region: PRK10651 998088003900 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 998088003901 active site 998088003902 phosphorylation site [posttranslational modification] 998088003903 intermolecular recognition site; other site 998088003904 dimerization interface [polypeptide binding]; other site 998088003905 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 998088003906 DNA binding residues [nucleotide binding] 998088003907 dimerization interface [polypeptide binding]; other site 998088003908 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 998088003909 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 998088003910 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 998088003911 dimerization interface [polypeptide binding]; other site 998088003912 Histidine kinase; Region: HisKA_3; pfam07730 998088003913 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 998088003914 ATP binding site [chemical binding]; other site 998088003915 Mg2+ binding site [ion binding]; other site 998088003916 G-X-G motif; other site 998088003917 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 998088003918 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 998088003919 FeS/SAM binding site; other site 998088003920 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 998088003921 ferredoxin-type protein; Provisional; Region: PRK10194 998088003922 4Fe-4S binding domain; Region: Fer4; pfam00037 998088003923 NapD protein; Region: NapD; pfam03927 998088003924 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 998088003925 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 998088003926 [4Fe-4S] binding site [ion binding]; other site 998088003927 molybdopterin cofactor binding site; other site 998088003928 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 998088003929 molybdopterin cofactor binding site; other site 998088003930 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 998088003931 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 998088003932 4Fe-4S binding domain; Region: Fer4_5; pfam12801 998088003933 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 998088003934 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 998088003935 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 998088003936 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 998088003937 MPT binding site; other site 998088003938 trimer interface [polypeptide binding]; other site 998088003939 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 998088003940 trimer interface [polypeptide binding]; other site 998088003941 dimer interface [polypeptide binding]; other site 998088003942 putative active site [active] 998088003943 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 998088003944 MoaE interaction surface [polypeptide binding]; other site 998088003945 MoeB interaction surface [polypeptide binding]; other site 998088003946 thiocarboxylated glycine; other site 998088003947 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 998088003948 MoaE homodimer interface [polypeptide binding]; other site 998088003949 MoaD interaction [polypeptide binding]; other site 998088003950 active site residues [active] 998088003951 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 998088003952 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 998088003953 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 998088003954 dimer interface [polypeptide binding]; other site 998088003955 ABC-ATPase subunit interface; other site 998088003956 putative PBP binding loops; other site 998088003957 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 998088003958 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088003959 Walker A/P-loop; other site 998088003960 ATP binding site [chemical binding]; other site 998088003961 Q-loop/lid; other site 998088003962 ABC transporter signature motif; other site 998088003963 Walker B; other site 998088003964 D-loop; other site 998088003965 H-loop/switch region; other site 998088003966 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088003967 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 998088003968 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 998088003969 ATP binding site [chemical binding]; other site 998088003970 substrate interface [chemical binding]; other site 998088003971 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 998088003972 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 998088003973 dimer interface [polypeptide binding]; other site 998088003974 putative functional site; other site 998088003975 putative MPT binding site; other site 998088003976 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 998088003977 GTP cyclohydrolase I; Provisional; Region: PLN03044 998088003978 active site 998088003979 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088003980 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 998088003981 dimerization interface [polypeptide binding]; other site 998088003982 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088003983 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088003984 dimer interface [polypeptide binding]; other site 998088003985 putative CheW interface [polypeptide binding]; other site 998088003986 formate--tetrahydrofolate ligase; Provisional; Region: PRK13506 998088003987 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 998088003988 Potassium binding sites [ion binding]; other site 998088003989 Cesium cation binding sites [ion binding]; other site 998088003990 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088003991 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088003992 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 998088003993 putative effector binding pocket; other site 998088003994 dimerization interface [polypeptide binding]; other site 998088003995 YceI-like domain; Region: YceI; cl01001 998088003996 S-adenosyl-L-homocysteine hydrolase, NAD binding domain; Region: AdoHcyase_NAD; smart00997 998088003997 NAD binding site [chemical binding]; other site 998088003998 Rdx family; Region: Rdx; cl01407 998088003999 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 998088004000 putative acyl-acceptor binding pocket; other site 998088004001 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 998088004002 peptidase T; Region: peptidase-T; TIGR01882 998088004003 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 998088004004 metal binding site [ion binding]; metal-binding site 998088004005 dimer interface [polypeptide binding]; other site 998088004006 arginine decarboxylase; Provisional; Region: PRK05354 998088004007 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 998088004008 dimer interface [polypeptide binding]; other site 998088004009 active site 998088004010 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088004011 catalytic residues [active] 998088004012 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 998088004013 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 998088004014 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 998088004015 SCP-2 sterol transfer family; Region: SCP2; pfam02036 998088004016 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088004017 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088004018 dimer interface [polypeptide binding]; other site 998088004019 putative CheW interface [polypeptide binding]; other site 998088004020 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088004021 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 998088004022 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 998088004023 homotrimer interaction site [polypeptide binding]; other site 998088004024 putative active site [active] 998088004025 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 998088004026 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 998088004027 YheO-like PAS domain; Region: PAS_6; pfam08348 998088004028 HTH domain; Region: HTH_22; pfam13309 998088004029 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 998088004030 catalytic core [active] 998088004031 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 998088004032 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 998088004033 non-specific DNA binding site [nucleotide binding]; other site 998088004034 salt bridge; other site 998088004035 sequence-specific DNA binding site [nucleotide binding]; other site 998088004036 Predicted transcriptional regulator [Transcription]; Region: COG2932 998088004037 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 998088004038 Catalytic site [active] 998088004039 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 998088004040 Integrase core domain; Region: rve; pfam00665 998088004041 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 998088004042 AAA ATPase domain; Region: AAA_16; pfam13191 998088004043 AAA domain; Region: AAA_22; pfam13401 998088004044 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 998088004045 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 998088004046 Mor transcription activator family; Region: Mor; cl02360 998088004047 Glycosyl hydrolase 108; Region: Glyco_hydro_108; pfam05838 998088004048 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 998088004049 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 998088004050 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 998088004051 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 998088004052 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 998088004053 Protein of unknown function (DUF935); Region: DUF935; pfam06074 998088004054 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 998088004055 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 998088004056 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; cl00083 998088004057 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 998088004058 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; pfam10124 998088004059 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 998088004060 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 998088004061 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 998088004062 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 998088004063 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 998088004064 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 998088004065 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 998088004066 aminotransferase AlaT; Validated; Region: PRK09265 998088004067 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 998088004068 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088004069 homodimer interface [polypeptide binding]; other site 998088004070 catalytic residue [active] 998088004071 Protein of unknown function (DUF1653); Region: DUF1653; pfam07866 998088004072 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 998088004073 amphipathic channel; other site 998088004074 Asn-Pro-Ala signature motifs; other site 998088004075 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 998088004076 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 998088004077 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088004078 catalytic residue [active] 998088004079 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088004080 Coenzyme A binding pocket [chemical binding]; other site 998088004081 Protein of unknown function (DUF1439); Region: DUF1439; pfam07273 998088004082 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 998088004083 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 998088004084 Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_1; cd09152 998088004085 putative active site [active] 998088004086 catalytic site [active] 998088004087 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_2; cd09158 998088004088 putative active site [active] 998088004089 catalytic site [active] 998088004090 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 998088004091 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 998088004092 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 998088004093 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 998088004094 putative active site [active] 998088004095 putative substrate binding site [chemical binding]; other site 998088004096 putative cosubstrate binding site; other site 998088004097 catalytic site [active] 998088004098 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK03353 998088004099 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 998088004100 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 998088004101 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 998088004102 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 998088004103 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 998088004104 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 998088004105 NlpC/P60 family; Region: NLPC_P60; pfam00877 998088004106 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 998088004107 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 998088004108 S-adenosylmethionine binding site [chemical binding]; other site 998088004109 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 998088004110 putative active site [active] 998088004111 putative catalytic site [active] 998088004112 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 998088004113 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 998088004114 transmembrane helices; other site 998088004115 Protein of unknown function, DUF481; Region: DUF481; cl01213 998088004116 L,D-transpeptidase; Provisional; Region: PRK10190 998088004117 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088004118 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 998088004119 Protein export membrane protein; Region: SecD_SecF; cl14618 998088004120 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 998088004121 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088004122 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088004123 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088004124 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 998088004125 active site 998088004126 phosphorylation site [posttranslational modification] 998088004127 intermolecular recognition site; other site 998088004128 dimerization interface [polypeptide binding]; other site 998088004129 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 998088004130 DNA binding site [nucleotide binding] 998088004131 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088004132 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 998088004133 dimerization interface [polypeptide binding]; other site 998088004134 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 998088004135 dimer interface [polypeptide binding]; other site 998088004136 phosphorylation site [posttranslational modification] 998088004137 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 998088004138 ATP binding site [chemical binding]; other site 998088004139 Mg2+ binding site [ion binding]; other site 998088004140 G-X-G motif; other site 998088004141 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 998088004142 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 998088004143 ATP binding site [chemical binding]; other site 998088004144 putative Mg++ binding site [ion binding]; other site 998088004145 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 998088004146 nucleotide binding region [chemical binding]; other site 998088004147 ATP-binding site [chemical binding]; other site 998088004148 DNA replication terminus site-binding protein (Ter protein); Region: Ter; pfam05472 998088004149 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 998088004150 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 998088004151 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 998088004152 putative active site [active] 998088004153 Zn binding site [ion binding]; other site 998088004154 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 998088004155 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 998088004156 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088004157 catalytic residue [active] 998088004158 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088004159 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088004160 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 998088004161 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088004162 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 998088004163 Methyltransferase domain; Region: Methyltransf_11; pfam08241 998088004164 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 998088004165 RNA/DNA hybrid binding site [nucleotide binding]; other site 998088004166 active site 998088004167 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 998088004168 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 998088004169 active site 998088004170 catalytic site [active] 998088004171 substrate binding site [chemical binding]; other site 998088004172 TIGR03503 family protein; Region: TIGR03503 998088004173 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088004174 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; cl17736 998088004175 active site 998088004176 phosphorylation site [posttranslational modification] 998088004177 intermolecular recognition site; other site 998088004178 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 998088004179 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 998088004180 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088004181 Zn2+ binding site [ion binding]; other site 998088004182 Mg2+ binding site [ion binding]; other site 998088004183 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 998088004184 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 998088004185 FAD binding pocket [chemical binding]; other site 998088004186 FAD binding motif [chemical binding]; other site 998088004187 phosphate binding motif [ion binding]; other site 998088004188 NAD binding pocket [chemical binding]; other site 998088004189 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 998088004190 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 998088004191 ABC-ATPase subunit interface; other site 998088004192 dimer interface [polypeptide binding]; other site 998088004193 putative PBP binding regions; other site 998088004194 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 998088004195 ABC-ATPase subunit interface; other site 998088004196 dimer interface [polypeptide binding]; other site 998088004197 putative PBP binding regions; other site 998088004198 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 998088004199 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 998088004200 Walker A/P-loop; other site 998088004201 ATP binding site [chemical binding]; other site 998088004202 Q-loop/lid; other site 998088004203 ABC transporter signature motif; other site 998088004204 Walker B; other site 998088004205 D-loop; other site 998088004206 H-loop/switch region; other site 998088004207 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 998088004208 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 998088004209 siderophore binding site; other site 998088004210 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 998088004211 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 998088004212 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 998088004213 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088004214 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 998088004215 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 998088004216 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088004217 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088004218 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 998088004219 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088004220 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088004221 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088004222 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 998088004223 putative catalytic site [active] 998088004224 putative phosphate binding site [ion binding]; other site 998088004225 active site 998088004226 metal binding site A [ion binding]; metal-binding site 998088004227 DNA binding site [nucleotide binding] 998088004228 putative AP binding site [nucleotide binding]; other site 998088004229 putative metal binding site B [ion binding]; other site 998088004230 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 998088004231 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 998088004232 Ion channel; Region: Ion_trans_2; pfam07885 998088004233 Response regulator receiver domain; Region: Response_reg; pfam00072 998088004234 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 998088004235 active site 998088004236 phosphorylation site [posttranslational modification] 998088004237 intermolecular recognition site; other site 998088004238 dimerization interface [polypeptide binding]; other site 998088004239 TPR repeat; Region: TPR_11; pfam13414 998088004240 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 998088004241 TPR motif; other site 998088004242 binding surface 998088004243 thiamine biosynthesis lipoprotein ApbE; Provisional; Region: PRK10461 998088004244 ApbE family; Region: ApbE; pfam02424 998088004245 azurin; Region: azurin; TIGR02695 998088004246 HutD; Region: HutD; pfam05962 998088004247 hypothetical protein; Provisional; Region: PRK11239 998088004248 Protein of unknown function, DUF480; Region: DUF480; pfam04337 998088004249 HAMP domain; Region: HAMP; pfam00672 998088004250 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088004251 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088004252 metal binding site [ion binding]; metal-binding site 998088004253 active site 998088004254 I-site; other site 998088004255 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 998088004256 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 998088004257 Protein of unknown function (DUF465); Region: DUF465; cl01070 998088004258 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 998088004259 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 998088004260 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 998088004261 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 998088004262 Sulfate transporter family; Region: Sulfate_transp; pfam00916 998088004263 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 998088004264 Bacterial protein of unknown function (DUF925); Region: DUF925; pfam06042 998088004265 Predicted acetyltransferase [General function prediction only]; Region: COG2388 998088004266 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 998088004267 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 998088004268 active site 998088004269 NAD binding site [chemical binding]; other site 998088004270 metal binding site [ion binding]; metal-binding site 998088004271 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088004272 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088004273 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 998088004274 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 998088004275 NAD(P) binding site [chemical binding]; other site 998088004276 catalytic residues [active] 998088004277 NH_hydro_CaPnhB: A subgroup of nucleoside hydrolases similar to Corynebacterium ammoniagenes Purine/pyrimidine nucleoside hydrolase (pnhB). Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These...; Region: nuc_hydro_CaPnhB; cd02650 998088004278 active site 998088004279 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 998088004280 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 998088004281 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 998088004282 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 998088004283 Protein of unknown function (DUF805); Region: DUF805; pfam05656 998088004284 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 998088004285 TPR motif; other site 998088004286 binding surface 998088004287 Uncharacterized conserved protein [Function unknown]; Region: COG1434 998088004288 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 998088004289 putative active site [active] 998088004290 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cd00091 998088004291 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 998088004292 active site 998088004293 substrate binding site [chemical binding]; other site 998088004294 Mg2+ binding site [ion binding]; other site 998088004295 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 998088004296 active site 998088004297 phosphorylation site [posttranslational modification] 998088004298 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; cl17425 998088004299 Phosphotransferase system, EIIC; Region: PTS_EIIC; pfam02378 998088004300 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 998088004301 active site 998088004302 P-loop; other site 998088004303 phosphorylation site [posttranslational modification] 998088004304 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088004305 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088004306 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 998088004307 dimerization interface [polypeptide binding]; other site 998088004308 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088004309 dimer interface [polypeptide binding]; other site 998088004310 putative CheW interface [polypeptide binding]; other site 998088004311 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 998088004312 mannose-6-phosphate isomerase; Provisional; Region: PRK15131 998088004313 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 998088004314 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088004315 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088004316 isocitrate dehydrogenase; Validated; Region: PRK07362 998088004317 isocitrate dehydrogenase; Reviewed; Region: PRK07006 998088004318 D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive...; Region: D-Ser-dehyd; cd06447 998088004319 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 998088004320 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088004321 catalytic residue [active] 998088004322 permease DsdX; Provisional; Region: PRK09921 998088004323 gluconate transporter; Region: gntP; TIGR00791 998088004324 DNA-binding transcriptional regulator DsdC; Provisional; Region: PRK10086 998088004325 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088004326 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 998088004327 dimerization interface [polypeptide binding]; other site 998088004328 substrate binding pocket [chemical binding]; other site 998088004329 NlpC/P60 family; Region: NLPC_P60; pfam00877 998088004330 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 998088004331 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088004332 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 998088004333 dimerization interface [polypeptide binding]; other site 998088004334 peroxidase; Provisional; Region: PRK15000 998088004335 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 998088004336 dimer interface [polypeptide binding]; other site 998088004337 decamer (pentamer of dimers) interface [polypeptide binding]; other site 998088004338 catalytic triad [active] 998088004339 peroxidatic and resolving cysteines [active] 998088004340 alpha-L-glutamate ligase-related protein; Region: rimK_rel_E_lig; TIGR02291 998088004341 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 998088004342 7 transmembrane helices usually fused to an inactive transglutaminase; Region: 7TM_transglut; pfam14402 998088004343 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 998088004344 Methyltransferase domain; Region: Methyltransf_23; pfam13489 998088004345 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 998088004346 S-adenosylmethionine binding site [chemical binding]; other site 998088004347 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 998088004348 S-adenosylmethionine binding site [chemical binding]; other site 998088004349 Protein of unknown function DUF72; Region: DUF72; cl00777 998088004350 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 998088004351 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 998088004352 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 998088004353 dimer interface [polypeptide binding]; other site 998088004354 anticodon binding site; other site 998088004355 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 998088004356 homodimer interface [polypeptide binding]; other site 998088004357 motif 1; other site 998088004358 active site 998088004359 motif 2; other site 998088004360 GAD domain; Region: GAD; pfam02938 998088004361 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 998088004362 active site 998088004363 motif 3; other site 998088004364 hypothetical protein; Validated; Region: PRK00110 998088004365 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 998088004366 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 998088004367 putative catalytic cysteine [active] 998088004368 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 998088004369 putative active site [active] 998088004370 metal binding site [ion binding]; metal-binding site 998088004371 hypothetical protein; Provisional; Region: PRK11111 998088004372 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 998088004373 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 998088004374 peptide binding site [polypeptide binding]; other site 998088004375 oligopeptide transporter permease; Reviewed; Region: oppB; PRK09471 998088004376 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 998088004377 dimer interface [polypeptide binding]; other site 998088004378 conserved gate region; other site 998088004379 putative PBP binding loops; other site 998088004380 ABC-ATPase subunit interface; other site 998088004381 oligopeptide ABC transporter permease OppC; Provisional; Region: PRK15406 998088004382 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 998088004383 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 998088004384 dimer interface [polypeptide binding]; other site 998088004385 conserved gate region; other site 998088004386 putative PBP binding loops; other site 998088004387 ABC-ATPase subunit interface; other site 998088004388 oligopeptide transporter ATP-binding component; Provisional; Region: oppD; PRK09473 998088004389 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088004390 Walker A/P-loop; other site 998088004391 ATP binding site [chemical binding]; other site 998088004392 Q-loop/lid; other site 998088004393 ABC transporter signature motif; other site 998088004394 Walker B; other site 998088004395 D-loop; other site 998088004396 H-loop/switch region; other site 998088004397 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 998088004398 oligopeptide ABC transporter ATP-binding protein OppF; Provisional; Region: PRK15079 998088004399 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088004400 Walker A/P-loop; other site 998088004401 ATP binding site [chemical binding]; other site 998088004402 Q-loop/lid; other site 998088004403 ABC transporter signature motif; other site 998088004404 Walker B; other site 998088004405 D-loop; other site 998088004406 H-loop/switch region; other site 998088004407 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 998088004408 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 998088004409 alanine racemase; Reviewed; Region: PRK13340 998088004410 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2; Region: PLPDE_III_AR2; cd06826 998088004411 active site 998088004412 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088004413 dimer interface [polypeptide binding]; other site 998088004414 substrate binding site [chemical binding]; other site 998088004415 catalytic residues [active] 998088004416 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 998088004417 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 998088004418 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 998088004419 Walker A motif; other site 998088004420 ATP binding site [chemical binding]; other site 998088004421 Walker B motif; other site 998088004422 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3169 998088004423 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 998088004424 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088004425 substrate binding pocket [chemical binding]; other site 998088004426 membrane-bound complex binding site; other site 998088004427 hinge residues; other site 998088004428 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 998088004429 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 998088004430 dimer interface [polypeptide binding]; other site 998088004431 putative PBP binding regions; other site 998088004432 ABC-ATPase subunit interface; other site 998088004433 vitamin B12-transporter ATPase; Provisional; Region: PRK03695 998088004434 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088004435 Walker A/P-loop; other site 998088004436 ATP binding site [chemical binding]; other site 998088004437 Q-loop/lid; other site 998088004438 ABC transporter signature motif; other site 998088004439 Walker B; other site 998088004440 D-loop; other site 998088004441 H-loop/switch region; other site 998088004442 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088004443 Coenzyme A binding pocket [chemical binding]; other site 998088004444 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12756 998088004445 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088004446 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 998088004447 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 998088004448 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 998088004449 ligand binding site [chemical binding]; other site 998088004450 NAD binding site [chemical binding]; other site 998088004451 tetramer interface [polypeptide binding]; other site 998088004452 catalytic site [active] 998088004453 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 998088004454 L-serine binding site [chemical binding]; other site 998088004455 ACT domain interface; other site 998088004456 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 998088004457 tetramer (dimer of dimers) interface [polypeptide binding]; other site 998088004458 active site 998088004459 dimer interface [polypeptide binding]; other site 998088004460 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 998088004461 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 998088004462 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 998088004463 H+/citrate symporter [Energy production and conversion]; Region: CitM; cl17620 998088004464 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 998088004465 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088004466 dihydrodipicolinate reductase; Provisional; Region: PRK00048 998088004467 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 998088004468 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 998088004469 carbamoyl-phosphate synthase, small subunit; Region: CPSaseIIsmall; TIGR01368 998088004470 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 998088004471 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 998088004472 catalytic site [active] 998088004473 subunit interface [polypeptide binding]; other site 998088004474 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 998088004475 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 998088004476 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 998088004477 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 998088004478 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 998088004479 ATP-grasp domain; Region: ATP-grasp_4; cl17255 998088004480 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 998088004481 IMP binding site; other site 998088004482 dimer interface [polypeptide binding]; other site 998088004483 interdomain contacts; other site 998088004484 partial ornithine binding site; other site 998088004485 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 998088004486 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 998088004487 chorismate mutase domain of T-protein; Region: CM_T; TIGR01799 998088004488 prephenate dehydrogenase; Provisional; Region: PRK06444 998088004489 prephenate dehydrogenase; Validated; Region: PRK08507 998088004490 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 998088004491 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088004492 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 998088004493 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 998088004494 ligand binding site; other site 998088004495 oligomer interface; other site 998088004496 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 998088004497 dimer interface [polypeptide binding]; other site 998088004498 N-terminal domain interface [polypeptide binding]; other site 998088004499 sulfate 1 binding site; other site 998088004500 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13021 998088004501 Protein export membrane protein; Region: SecD_SecF; pfam02355 998088004502 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 998088004503 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 998088004504 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 998088004505 thiamine kinase; Region: ycfN_thiK; TIGR02721 998088004506 active site 998088004507 substrate binding site [chemical binding]; other site 998088004508 ATP binding site [chemical binding]; other site 998088004509 Protein of unknown function (DUF3897); Region: DUF3897; pfam13036 998088004510 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 998088004511 putative dimer interface [polypeptide binding]; other site 998088004512 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 998088004513 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 998088004514 nucleotide binding site/active site [active] 998088004515 HIT family signature motif; other site 998088004516 catalytic residue [active] 998088004517 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 998088004518 dimerization interface [polypeptide binding]; other site 998088004519 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088004520 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088004521 dimer interface [polypeptide binding]; other site 998088004522 putative CheW interface [polypeptide binding]; other site 998088004523 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 998088004524 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 998088004525 dihydroorotase; Reviewed; Region: PRK09236 998088004526 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 998088004527 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 998088004528 active site 998088004529 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 998088004530 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 998088004531 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088004532 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088004533 HAMP domain; Region: HAMP; pfam00672 998088004534 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088004535 dimer interface [polypeptide binding]; other site 998088004536 putative CheW interface [polypeptide binding]; other site 998088004537 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 998088004538 Protein of unknown function (DUF808); Region: DUF808; cl01002 998088004539 Protein of unknown function (DUF808); Region: DUF808; pfam05661 998088004540 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 998088004541 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_2; cd09607 998088004542 active site 998088004543 Zn binding site [ion binding]; other site 998088004544 xanthine permease; Region: pbuX; TIGR03173 998088004545 hypothetical protein; Provisional; Region: PRK04940 998088004546 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 998088004547 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088004548 Predicted membrane protein [Function unknown]; Region: COG3235 998088004549 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 998088004550 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 998088004551 FeS/SAM binding site; other site 998088004552 GAF domain; Region: GAF; pfam01590 998088004553 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 998088004554 PAS domain; Region: PAS_9; pfam13426 998088004555 putative active site [active] 998088004556 heme pocket [chemical binding]; other site 998088004557 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088004558 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088004559 metal binding site [ion binding]; metal-binding site 998088004560 active site 998088004561 I-site; other site 998088004562 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 998088004563 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 998088004564 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088004565 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088004566 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088004567 Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar...; Region: RHOD_Pyr_redox; cd01524 998088004568 active site residue [active] 998088004569 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 998088004570 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 998088004571 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 998088004572 MG2 domain; Region: A2M_N; pfam01835 998088004573 Alpha-2-macroglobulin family; Region: A2M; pfam00207 998088004574 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 998088004575 surface patch; other site 998088004576 thioester region; other site 998088004577 penicillin-binding protein 1C; Provisional; Region: PRK11240 998088004578 Transglycosylase; Region: Transgly; pfam00912 998088004579 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 998088004580 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 998088004581 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 998088004582 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 998088004583 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 998088004584 Ligand Binding Site [chemical binding]; other site 998088004585 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 998088004586 active site residue [active] 998088004587 hypothetical protein; Provisional; Region: PRK10578 998088004588 UPF0126 domain; Region: UPF0126; pfam03458 998088004589 UPF0126 domain; Region: UPF0126; pfam03458 998088004590 flagellin; Provisional; Region: PRK12802 998088004591 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 998088004592 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 998088004593 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 998088004594 flagellin; Provisional; Region: PRK12802 998088004595 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 998088004596 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 998088004597 flagellin; Provisional; Region: PRK12802 998088004598 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 998088004599 flagellar capping protein; Reviewed; Region: fliD; PRK08032 998088004600 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 998088004601 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 998088004602 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 998088004603 Flagellar protein FliS; Region: FliS; cl00654 998088004604 Protein of unknown function DUF115; Region: MAF_flag10; pfam01973 998088004605 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088004606 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 998088004607 Transposase; Region: DEDD_Tnp_IS110; pfam01548 998088004608 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 998088004609 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 998088004610 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 998088004611 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 998088004612 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor...; Region: BtuF; cd01144 998088004613 cobalamin binding residues [chemical binding]; other site 998088004614 putative BtuC binding residues; other site 998088004615 dimer interface [polypeptide binding]; other site 998088004616 CobD/Cbib protein; Region: CobD_Cbib; cl00561 998088004617 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 998088004618 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 998088004619 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 998088004620 ZIP Zinc transporter; Region: Zip; pfam02535 998088004621 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088004622 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088004623 HAMP domain; Region: HAMP; pfam00672 998088004624 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088004625 dimer interface [polypeptide binding]; other site 998088004626 putative CheW interface [polypeptide binding]; other site 998088004627 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 998088004628 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 998088004629 active site 998088004630 dimerization interface [polypeptide binding]; other site 998088004631 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 998088004632 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 998088004633 C-terminal domain interface [polypeptide binding]; other site 998088004634 GSH binding site (G-site) [chemical binding]; other site 998088004635 dimer interface [polypeptide binding]; other site 998088004636 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 998088004637 N-terminal domain interface [polypeptide binding]; other site 998088004638 dimer interface [polypeptide binding]; other site 998088004639 substrate binding pocket (H-site) [chemical binding]; other site 998088004640 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 998088004641 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 998088004642 putative substrate translocation pore; other site 998088004643 Cell division protein ZapA; Region: ZapA; cl01146 998088004644 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 998088004645 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 998088004646 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK05732 998088004647 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 998088004648 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 998088004649 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 998088004650 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 998088004651 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 998088004652 lipoyl attachment site [posttranslational modification]; other site 998088004653 glycine dehydrogenase; Provisional; Region: PRK05367 998088004654 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 998088004655 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088004656 catalytic residue [active] 998088004657 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 998088004658 tetramer interface [polypeptide binding]; other site 998088004659 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088004660 catalytic residue [active] 998088004661 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 998088004662 PAS fold; Region: PAS_3; pfam08447 998088004663 putative active site [active] 998088004664 heme pocket [chemical binding]; other site 998088004665 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088004666 dimer interface [polypeptide binding]; other site 998088004667 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 998088004668 putative CheW interface [polypeptide binding]; other site 998088004669 Predicted permease; Region: DUF318; cl17795 998088004670 Predicted permease; Region: DUF318; cl17795 998088004671 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 998088004672 dimerization interface [polypeptide binding]; other site 998088004673 putative DNA binding site [nucleotide binding]; other site 998088004674 putative Zn2+ binding site [ion binding]; other site 998088004675 aromatic amino acid transporter; Provisional; Region: PRK10238 998088004676 PEP synthetase regulatory protein; Provisional; Region: PRK05339 998088004677 phosphoenolpyruvate synthase; Validated; Region: PRK06464 998088004678 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 998088004679 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 998088004680 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 998088004681 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 998088004682 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl17414 998088004683 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088004684 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088004685 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 998088004686 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 998088004687 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 998088004688 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 998088004689 Peptidase S8 family domain in Protein convertases; Region: Peptidases_S8_Protein_convertases_Kexins_Furin-lik; cd04059 998088004690 calcium binding site 1 [ion binding]; other site 998088004691 active site 998088004692 catalytic triad [active] 998088004693 calcium binding site 2 [ion binding]; other site 998088004694 calcium binding site 3 [ion binding]; other site 998088004695 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 998088004696 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 998088004697 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 998088004698 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 998088004699 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 998088004700 Sulfatase; Region: Sulfatase; cl17466 998088004701 hypothetical protein; Provisional; Region: PRK13689 998088004702 Nucleoid-associated protein [General function prediction only]; Region: COG3081 998088004703 nucleoid-associated protein NdpA; Validated; Region: PRK00378 998088004704 maltose ABC transporter periplasmic protein; Reviewed; Region: malE; PRK09474 998088004705 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 998088004706 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 998088004707 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 998088004708 dimer interface [polypeptide binding]; other site 998088004709 conserved gate region; other site 998088004710 putative PBP binding loops; other site 998088004711 ABC-ATPase subunit interface; other site 998088004712 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 998088004713 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 998088004714 dimer interface [polypeptide binding]; other site 998088004715 conserved gate region; other site 998088004716 putative PBP binding loops; other site 998088004717 ABC-ATPase subunit interface; other site 998088004718 maltose/maltodextrin transporter ATP-binding protein; Provisional; Region: PRK11000 998088004719 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 998088004720 Walker A/P-loop; other site 998088004721 ATP binding site [chemical binding]; other site 998088004722 Q-loop/lid; other site 998088004723 ABC transporter signature motif; other site 998088004724 Walker B; other site 998088004725 D-loop; other site 998088004726 H-loop/switch region; other site 998088004727 TOBE domain; Region: TOBE; pfam03459 998088004728 TOBE domain; Region: TOBE_2; pfam08402 998088004729 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 998088004730 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 998088004731 MltA-interacting protein MipA; Region: MipA; cl01504 998088004732 Domain of unknown function DUF20; Region: UPF0118; pfam01594 998088004733 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 998088004734 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 998088004735 CPxP motif; other site 998088004736 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 998088004737 Peptidase family M48; Region: Peptidase_M48; pfam01435 998088004738 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 998088004739 binding surface 998088004740 TPR motif; other site 998088004741 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 998088004742 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 998088004743 catalytic residues [active] 998088004744 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 998088004745 ArsC family; Region: ArsC; pfam03960 998088004746 catalytic residues [active] 998088004747 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 998088004748 Protein of unknown function, DUF479; Region: DUF479; cl01203 998088004749 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 998088004750 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 998088004751 substrate binding pocket [chemical binding]; other site 998088004752 membrane-bound complex binding site; other site 998088004753 hinge residues; other site 998088004754 isoaspartyl dipeptidase; Provisional; Region: PRK10657 998088004755 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 998088004756 active site 998088004757 Predicted membrane protein [Function unknown]; Region: COG2431 998088004758 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 998088004759 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 998088004760 Walker A/P-loop; other site 998088004761 ATP binding site [chemical binding]; other site 998088004762 Q-loop/lid; other site 998088004763 ABC transporter signature motif; other site 998088004764 Walker B; other site 998088004765 D-loop; other site 998088004766 H-loop/switch region; other site 998088004767 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 998088004768 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 998088004769 substrate binding pocket [chemical binding]; other site 998088004770 membrane-bound complex binding site; other site 998088004771 hinge residues; other site 998088004772 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088004773 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 998088004774 dimer interface [polypeptide binding]; other site 998088004775 conserved gate region; other site 998088004776 putative PBP binding loops; other site 998088004777 ABC-ATPase subunit interface; other site 998088004778 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088004779 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 998088004780 dimer interface [polypeptide binding]; other site 998088004781 conserved gate region; other site 998088004782 putative PBP binding loops; other site 998088004783 ABC-ATPase subunit interface; other site 998088004784 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 998088004785 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 998088004786 active site 998088004787 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 998088004788 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 998088004789 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 998088004790 dimer interface [polypeptide binding]; other site 998088004791 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 998088004792 active site 998088004793 Fe binding site [ion binding]; other site 998088004794 homogentisate 1,2-dioxygenase; Region: HgmA; cl17306 998088004795 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 998088004796 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 998088004797 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 998088004798 maleylacetoacetate isomerase; Region: maiA; TIGR01262 998088004799 C-terminal domain interface [polypeptide binding]; other site 998088004800 GSH binding site (G-site) [chemical binding]; other site 998088004801 putative dimer interface [polypeptide binding]; other site 998088004802 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 998088004803 dimer interface [polypeptide binding]; other site 998088004804 N-terminal domain interface [polypeptide binding]; other site 998088004805 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 998088004806 Peptidase family C69; Region: Peptidase_C69; cl17793 998088004807 peptidase T; Region: peptidase-T; TIGR01882 998088004808 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 998088004809 metal binding site [ion binding]; metal-binding site 998088004810 dimer interface [polypeptide binding]; other site 998088004811 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; cl17322 998088004812 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 998088004813 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 998088004814 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 998088004815 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 998088004816 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 998088004817 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 998088004818 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 998088004819 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088004820 ABC transporter signature motif; other site 998088004821 Walker B; other site 998088004822 D-loop; other site 998088004823 H-loop/switch region; other site 998088004824 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 998088004825 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 998088004826 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 998088004827 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 998088004828 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088004829 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 998088004830 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 998088004831 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 998088004832 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 998088004833 Glycosyl transferase family 2; Region: Glyco_tranf_2_4; pfam13704 998088004834 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 998088004835 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 998088004836 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 998088004837 active site 998088004838 tetramer interface; other site 998088004839 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 998088004840 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 998088004841 NAD binding site [chemical binding]; other site 998088004842 substrate binding site [chemical binding]; other site 998088004843 homodimer interface [polypeptide binding]; other site 998088004844 active site 998088004845 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 998088004846 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 998088004847 NADP binding site [chemical binding]; other site 998088004848 active site 998088004849 putative substrate binding site [chemical binding]; other site 998088004850 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 998088004851 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 998088004852 substrate binding site; other site 998088004853 tetramer interface; other site 998088004854 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 998088004855 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsC; COG3563 998088004856 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 998088004857 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 998088004858 asparagine synthetase B; Provisional; Region: asnB; PRK09431 998088004859 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 998088004860 active site 998088004861 dimer interface [polypeptide binding]; other site 998088004862 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 998088004863 Ligand Binding Site [chemical binding]; other site 998088004864 Molecular Tunnel; other site 998088004865 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 998088004866 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 998088004867 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 998088004868 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 998088004869 TrkA-N domain; Region: TrkA_N; pfam02254 998088004870 UMP phosphatase; Provisional; Region: PRK10444 998088004871 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 998088004872 active site 998088004873 motif I; other site 998088004874 motif II; other site 998088004875 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 998088004876 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 998088004877 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 998088004878 active site 998088004879 purine riboside binding site [chemical binding]; other site 998088004880 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR5; cd08271 998088004881 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 998088004882 putative NAD(P) binding site [chemical binding]; other site 998088004883 substrate binding site [chemical binding]; other site 998088004884 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 998088004885 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 998088004886 FMN binding site [chemical binding]; other site 998088004887 active site 998088004888 substrate binding site [chemical binding]; other site 998088004889 catalytic residue [active] 998088004890 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 998088004891 FOG: CBS domain [General function prediction only]; Region: COG0517 998088004892 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 998088004893 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 998088004894 Cation efflux family; Region: Cation_efflux; cl00316 998088004895 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 998088004896 FAD binding domain; Region: FAD_binding_4; pfam01565 998088004897 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 998088004898 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 998088004899 CoenzymeA binding site [chemical binding]; other site 998088004900 subunit interaction site [polypeptide binding]; other site 998088004901 PHB binding site; other site 998088004902 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 998088004903 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 998088004904 ATP binding site [chemical binding]; other site 998088004905 Mg++ binding site [ion binding]; other site 998088004906 motif III; other site 998088004907 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 998088004908 nucleotide binding region [chemical binding]; other site 998088004909 ATP-binding site [chemical binding]; other site 998088004910 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 998088004911 putative RNA binding site [nucleotide binding]; other site 998088004912 Predicted permease [General function prediction only]; Region: COG2056 998088004913 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 998088004914 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; cl17322 998088004915 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 998088004916 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 998088004917 dimer interface [polypeptide binding]; other site 998088004918 catalytic site [active] 998088004919 putative active site [active] 998088004920 putative substrate binding site [chemical binding]; other site 998088004921 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 998088004922 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 998088004923 active site 998088004924 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 998088004925 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 998088004926 ligand binding site [chemical binding]; other site 998088004927 NAD binding site [chemical binding]; other site 998088004928 catalytic site [active] 998088004929 homodimer interface [polypeptide binding]; other site 998088004930 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 998088004931 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 998088004932 FimV N-terminal domain; Region: FimV_core; TIGR03505 998088004933 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 998088004934 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 998088004935 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 998088004936 dimerization interface 3.5A [polypeptide binding]; other site 998088004937 active site 998088004938 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 998088004939 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 998088004940 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 998088004941 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 998088004942 Sporulation related domain; Region: SPOR; pfam05036 998088004943 hypothetical protein; Provisional; Region: PRK02877 998088004944 siroheme synthase; Provisional; Region: cysG; PRK10637 998088004945 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 998088004946 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 998088004947 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 998088004948 active site 998088004949 SAM binding site [chemical binding]; other site 998088004950 homodimer interface [polypeptide binding]; other site 998088004951 sulfite reductase, subunit C; Region: sulfite_red_C; TIGR02912 998088004952 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 998088004953 4Fe-4S binding domain; Region: Fer4_6; pfam12837 998088004954 4Fe-4S binding domain; Region: Fer4; pfam00037 998088004955 anaerobic sulfite reductase subunit B; Provisional; Region: PRK08221 998088004956 Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is...; Region: sulfite_reductase_like; cd06221 998088004957 FAD binding pocket [chemical binding]; other site 998088004958 FAD binding motif [chemical binding]; other site 998088004959 phosphate binding motif [ion binding]; other site 998088004960 beta-alpha-beta structure motif; other site 998088004961 NAD binding pocket [chemical binding]; other site 998088004962 Iron coordination center [ion binding]; other site 998088004963 anaerobic sulfite reductase subunit A; Provisional; Region: PRK15055 998088004964 putative encapsidation protein; Region: PHA01076 998088004965 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 998088004966 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 998088004967 active site 998088004968 nucleophile elbow; other site 998088004969 Microcin C7 self-immunity protein determines resistance to exogenous microcin C7; Region: Peptidase_S66_mccF_like; cd07062 998088004970 putative dimer interface [polypeptide binding]; other site 998088004971 catalytic triad [active] 998088004972 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 998088004973 Sulfatase; Region: Sulfatase; cl17466 998088004974 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 998088004975 active site 998088004976 substrate binding site [chemical binding]; other site 998088004977 ATP binding site [chemical binding]; other site 998088004978 aspartate kinase III; Validated; Region: PRK09084 998088004979 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 998088004980 nucleotide binding site [chemical binding]; other site 998088004981 substrate binding site [chemical binding]; other site 998088004982 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_1; cd04932 998088004983 lysine allosteric regulatory site; other site 998088004984 dimer interface [polypeptide binding]; other site 998088004985 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 998088004986 dimer interface [polypeptide binding]; other site 998088004987 N-acetylglutamate synthase; Validated; Region: PRK05279 998088004988 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 998088004989 putative feedback inhibition sensing region; other site 998088004990 putative nucleotide binding site [chemical binding]; other site 998088004991 putative substrate binding site [chemical binding]; other site 998088004992 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088004993 Coenzyme A binding pocket [chemical binding]; other site 998088004994 methionine sulfoxide reductase A; Provisional; Region: PRK00058 998088004995 Protein of unknown function (DUF3802); Region: DUF3802; pfam12290 998088004996 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 998088004997 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 998088004998 Uncharacterized protein conserved in bacteria [Function unknown]; Region: MmcQ; COG2315 998088004999 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 998088005000 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088005001 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 998088005002 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 998088005003 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088005004 FtsX-like permease family; Region: FtsX; pfam02687 998088005005 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 998088005006 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 998088005007 Walker A/P-loop; other site 998088005008 ATP binding site [chemical binding]; other site 998088005009 Q-loop/lid; other site 998088005010 ABC transporter signature motif; other site 998088005011 Walker B; other site 998088005012 D-loop; other site 998088005013 H-loop/switch region; other site 998088005014 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 998088005015 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 998088005016 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 998088005017 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 998088005018 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 998088005019 putative substrate translocation pore; other site 998088005020 hypothetical protein; Provisional; Region: PRK07208 998088005021 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 998088005022 UDP-galactopyranose mutase; Region: GLF; pfam03275 998088005023 Iron permease FTR1 family; Region: FTR1; cl00475 998088005024 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 998088005025 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 998088005026 Integrase core domain; Region: rve_3; pfam13683 998088005027 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 998088005028 putative transporter; Provisional; Region: PRK11660 998088005029 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 998088005030 Sulfate transporter family; Region: Sulfate_transp; pfam00916 998088005031 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 998088005032 recombination protein RecR; Reviewed; Region: recR; PRK00076 998088005033 RecR protein; Region: RecR; pfam02132 998088005034 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 998088005035 putative active site [active] 998088005036 putative metal-binding site [ion binding]; other site 998088005037 tetramer interface [polypeptide binding]; other site 998088005038 heat shock protein 90; Provisional; Region: PRK05218 998088005039 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 998088005040 ATP binding site [chemical binding]; other site 998088005041 Mg2+ binding site [ion binding]; other site 998088005042 G-X-G motif; other site 998088005043 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 998088005044 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088005045 Walker A/P-loop; other site 998088005046 ATP binding site [chemical binding]; other site 998088005047 Q-loop/lid; other site 998088005048 ABC transporter signature motif; other site 998088005049 Walker B; other site 998088005050 D-loop; other site 998088005051 H-loop/switch region; other site 998088005052 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapD; COG4170 998088005053 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088005054 Walker A/P-loop; other site 998088005055 ATP binding site [chemical binding]; other site 998088005056 Q-loop/lid; other site 998088005057 ABC transporter signature motif; other site 998088005058 Walker B; other site 998088005059 D-loop; other site 998088005060 H-loop/switch region; other site 998088005061 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088005062 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 998088005063 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 998088005064 putative PBP binding loops; other site 998088005065 dimer interface [polypeptide binding]; other site 998088005066 ABC-ATPase subunit interface; other site 998088005067 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 998088005068 dimer interface [polypeptide binding]; other site 998088005069 conserved gate region; other site 998088005070 putative PBP binding loops; other site 998088005071 ABC-ATPase subunit interface; other site 998088005072 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 998088005073 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 998088005074 peptide binding site [polypeptide binding]; other site 998088005075 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 998088005076 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 998088005077 Walker A motif; other site 998088005078 ATP binding site [chemical binding]; other site 998088005079 Walker B motif; other site 998088005080 arginine finger; other site 998088005081 phage shock protein A; Region: phageshock_pspA; TIGR02977 998088005082 phage shock protein B; Provisional; Region: pspB; PRK09458 998088005083 PspC domain; Region: PspC; cl00864 998088005084 phage shock protein C; Region: phageshock_pspC; TIGR02978 998088005085 YcjX-like family, DUF463; Region: DUF463; pfam04317 998088005086 hypothetical protein; Provisional; Region: PRK05415 998088005087 Domain of unknown function (DUF697); Region: DUF697; cl12064 998088005088 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088005089 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088005090 The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_PAO1_like; cd08412 998088005091 putative substrate binding pocket [chemical binding]; other site 998088005092 dimerization interface [polypeptide binding]; other site 998088005093 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 998088005094 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 998088005095 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 998088005096 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088005097 Walker A/P-loop; other site 998088005098 ATP binding site [chemical binding]; other site 998088005099 Q-loop/lid; other site 998088005100 ABC transporter signature motif; other site 998088005101 Walker B; other site 998088005102 D-loop; other site 998088005103 H-loop/switch region; other site 998088005104 TOBE domain; Region: TOBE_2; pfam08402 998088005105 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 998088005106 dimer interface [polypeptide binding]; other site 998088005107 conserved gate region; other site 998088005108 putative PBP binding loops; other site 998088005109 ABC-ATPase subunit interface; other site 998088005110 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 998088005111 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 998088005112 dimer interface [polypeptide binding]; other site 998088005113 conserved gate region; other site 998088005114 putative PBP binding loops; other site 998088005115 ABC-ATPase subunit interface; other site 998088005116 gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK13473 998088005117 Escherichia coli NAD+-dependent gamma-aminobutyraldehyde dehydrogenase YdcW-like; Region: ALDH_ABALDH-YdcW; cd07092 998088005118 tetrameric interface [polypeptide binding]; other site 998088005119 NAD binding site [chemical binding]; other site 998088005120 catalytic residues [active] 998088005121 substrate binding site [chemical binding]; other site 998088005122 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 998088005123 cofactor binding site; other site 998088005124 metal binding site [ion binding]; metal-binding site 998088005125 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_subfamily_a; cd00913 998088005126 aromatic arch; other site 998088005127 DCoH dimer interaction site [polypeptide binding]; other site 998088005128 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 998088005129 DCoH tetramer interaction site [polypeptide binding]; other site 998088005130 substrate binding site [chemical binding]; other site 998088005131 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 998088005132 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 998088005133 putative aromatic amino acid binding site; other site 998088005134 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 998088005135 putative active site [active] 998088005136 heme pocket [chemical binding]; other site 998088005137 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 998088005138 Walker A motif; other site 998088005139 ATP binding site [chemical binding]; other site 998088005140 Walker B motif; other site 998088005141 arginine finger; other site 998088005142 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 998088005143 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 998088005144 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 998088005145 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088005146 metal binding site [ion binding]; metal-binding site 998088005147 active site 998088005148 I-site; other site 998088005149 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088005150 ligand binding site [chemical binding]; other site 998088005151 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 998088005152 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 998088005153 YfcL protein; Region: YfcL; pfam08891 998088005154 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 998088005155 Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase; Region: LC_FACS_bac; cd05932 998088005156 acyl-activating enzyme (AAE) consensus motif; other site 998088005157 putative AMP binding site [chemical binding]; other site 998088005158 putative active site [active] 998088005159 putative CoA binding site [chemical binding]; other site 998088005160 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 998088005161 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 998088005162 homodimer interface [polypeptide binding]; other site 998088005163 substrate-cofactor binding pocket; other site 998088005164 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088005165 catalytic residue [active] 998088005166 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 998088005167 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 998088005168 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 998088005169 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 998088005170 NADH(P)-binding; Region: NAD_binding_10; pfam13460 998088005171 NAD binding site [chemical binding]; other site 998088005172 substrate binding site [chemical binding]; other site 998088005173 putative active site [active] 998088005174 transcriptional regulator; Provisional; Region: PRK10632 998088005175 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088005176 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 998088005177 putative effector binding pocket; other site 998088005178 dimerization interface [polypeptide binding]; other site 998088005179 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 998088005180 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088005181 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 998088005182 dimerization interface [polypeptide binding]; other site 998088005183 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 998088005184 Major Facilitator Superfamily; Region: MFS_1; pfam07690 998088005185 putative substrate translocation pore; other site 998088005186 Pirin-related protein [General function prediction only]; Region: COG1741 998088005187 Pirin; Region: Pirin; pfam02678 998088005188 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 998088005189 Isochorismatase family; Region: Isochorismatase; pfam00857 998088005190 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 998088005191 catalytic triad [active] 998088005192 dimer interface [polypeptide binding]; other site 998088005193 conserved cis-peptide bond; other site 998088005194 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088005195 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 998088005196 putative effector binding pocket; other site 998088005197 dimerization interface [polypeptide binding]; other site 998088005198 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088005199 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088005200 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 998088005201 putative dimerization interface [polypeptide binding]; other site 998088005202 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 998088005203 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 998088005204 THF binding site; other site 998088005205 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 998088005206 substrate binding site [chemical binding]; other site 998088005207 THF binding site; other site 998088005208 zinc-binding site [ion binding]; other site 998088005209 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 998088005210 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088005211 substrate binding pocket [chemical binding]; other site 998088005212 membrane-bound complex binding site; other site 998088005213 hinge residues; other site 998088005214 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088005215 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088005216 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 998088005217 dimerization interface [polypeptide binding]; other site 998088005218 substrate binding pocket [chemical binding]; other site 998088005219 Beta-glucosidase/6-phospho-beta-glucosidase/beta- galactosidase [Carbohydrate transport and metabolism]; Region: BglB; COG2723 998088005220 beta-galactosidase; Region: BGL; TIGR03356 998088005221 uncharacterized domain; Region: TIGR00702 998088005222 YcaO-like family; Region: YcaO; pfam02624 998088005223 formate transporter FocA; Region: formate_focA; TIGR04060 998088005224 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 998088005225 Pyruvate formate lyase 1; Region: PFL1; cd01678 998088005226 coenzyme A binding site [chemical binding]; other site 998088005227 active site 998088005228 catalytic residues [active] 998088005229 glycine loop; other site 998088005230 hypothetical protein; Provisional; Region: PRK05170 998088005231 Cell division inhibitor SulA; Region: SulA; cl01880 998088005232 Domain of unknown function (DUF4250); Region: DUF4250; pfam14056 998088005233 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 998088005234 homodimer interface [polypeptide binding]; other site 998088005235 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 998088005236 active site pocket [active] 998088005237 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 998088005238 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 998088005239 transmembrane helices; other site 998088005240 thioredoxin 2; Provisional; Region: PRK10996 998088005241 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 998088005242 catalytic residues [active] 998088005243 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088005244 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 998088005245 dimer interface [polypeptide binding]; other site 998088005246 phosphorylation site [posttranslational modification] 998088005247 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 998088005248 ATP binding site [chemical binding]; other site 998088005249 Mg2+ binding site [ion binding]; other site 998088005250 G-X-G motif; other site 998088005251 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088005252 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 998088005253 active site 998088005254 phosphorylation site [posttranslational modification] 998088005255 intermolecular recognition site; other site 998088005256 dimerization interface [polypeptide binding]; other site 998088005257 Response regulator receiver domain; Region: Response_reg; pfam00072 998088005258 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 998088005259 active site 998088005260 phosphorylation site [posttranslational modification] 998088005261 intermolecular recognition site; other site 998088005262 dimerization interface [polypeptide binding]; other site 998088005263 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 998088005264 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 998088005265 putative multidrug transporter membrane\ATP-binding components; Provisional; Region: PRK10789 998088005266 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088005267 Walker A/P-loop; other site 998088005268 ATP binding site [chemical binding]; other site 998088005269 Q-loop/lid; other site 998088005270 ABC transporter signature motif; other site 998088005271 Walker B; other site 998088005272 D-loop; other site 998088005273 H-loop/switch region; other site 998088005274 putative multidrug transporter membrane\ATP-binding components; Provisional; Region: PRK10790 998088005275 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 998088005276 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088005277 Walker A/P-loop; other site 998088005278 ATP binding site [chemical binding]; other site 998088005279 Q-loop/lid; other site 998088005280 ABC transporter signature motif; other site 998088005281 Walker B; other site 998088005282 D-loop; other site 998088005283 H-loop/switch region; other site 998088005284 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 998088005285 active site 1 [active] 998088005286 S4 domain; Region: S4_2; cl17325 998088005287 pyridoxamine kinase; Validated; Region: PRK05756 998088005288 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 998088005289 dimer interface [polypeptide binding]; other site 998088005290 pyridoxal binding site [chemical binding]; other site 998088005291 ATP binding site [chemical binding]; other site 998088005292 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 998088005293 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 998088005294 dimer interface [polypeptide binding]; other site 998088005295 active site 998088005296 metal binding site [ion binding]; metal-binding site 998088005297 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088005298 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 998088005299 Coenzyme A binding pocket [chemical binding]; other site 998088005300 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_31; cd04690 998088005301 nudix motif; other site 998088005302 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 998088005303 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088005304 Coenzyme A binding pocket [chemical binding]; other site 998088005305 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 998088005306 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 998088005307 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 998088005308 dimer interface [polypeptide binding]; other site 998088005309 active site 998088005310 citrylCoA binding site [chemical binding]; other site 998088005311 NADH binding [chemical binding]; other site 998088005312 cationic pore residues; other site 998088005313 oxalacetate/citrate binding site [chemical binding]; other site 998088005314 coenzyme A binding site [chemical binding]; other site 998088005315 catalytic triad [active] 998088005316 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 998088005317 Iron-sulfur protein interface; other site 998088005318 proximal quinone binding site [chemical binding]; other site 998088005319 SdhD (CybS) interface [polypeptide binding]; other site 998088005320 proximal heme binding site [chemical binding]; other site 998088005321 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 998088005322 SdhC subunit interface [polypeptide binding]; other site 998088005323 proximal heme binding site [chemical binding]; other site 998088005324 cardiolipin binding site; other site 998088005325 Iron-sulfur protein interface; other site 998088005326 proximal quinone binding site [chemical binding]; other site 998088005327 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 998088005328 L-aspartate oxidase; Provisional; Region: PRK06175 998088005329 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 998088005330 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 998088005331 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 998088005332 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 998088005333 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 998088005334 TPP-binding site [chemical binding]; other site 998088005335 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 998088005336 dimer interface [polypeptide binding]; other site 998088005337 PYR/PP interface [polypeptide binding]; other site 998088005338 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 998088005339 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 998088005340 E3 interaction surface; other site 998088005341 lipoyl attachment site [posttranslational modification]; other site 998088005342 e3 binding domain; Region: E3_binding; pfam02817 998088005343 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 998088005344 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 998088005345 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 998088005346 CoA-ligase; Region: Ligase_CoA; pfam00549 998088005347 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 998088005348 CoA binding domain; Region: CoA_binding; pfam02629 998088005349 CoA-ligase; Region: Ligase_CoA; pfam00549 998088005350 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 998088005351 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088005352 putative 2-aminoethylphosphonate ABC transporter, permease protein; Region: PhnU2; TIGR03262 998088005353 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 998088005354 dimer interface [polypeptide binding]; other site 998088005355 conserved gate region; other site 998088005356 putative PBP binding loops; other site 998088005357 ABC-ATPase subunit interface; other site 998088005358 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 998088005359 dimer interface [polypeptide binding]; other site 998088005360 conserved gate region; other site 998088005361 putative PBP binding loops; other site 998088005362 ABC-ATPase subunit interface; other site 998088005363 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein; Region: PhnT2; TIGR03265 998088005364 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088005365 Walker A/P-loop; other site 998088005366 ATP binding site [chemical binding]; other site 998088005367 Q-loop/lid; other site 998088005368 ABC transporter signature motif; other site 998088005369 Walker B; other site 998088005370 D-loop; other site 998088005371 H-loop/switch region; other site 998088005372 TOBE domain; Region: TOBE_2; pfam08402 998088005373 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 998088005374 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 998088005375 transcriptional regulator protein; Region: phnR; TIGR03337 998088005376 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088005377 DNA-binding site [nucleotide binding]; DNA binding site 998088005378 UTRA domain; Region: UTRA; pfam07702 998088005379 2-aminoethylphosphonate--pyruvate transaminase; Provisional; Region: PRK13479 998088005380 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088005381 catalytic residue [active] 998088005382 4-aminobutyrate aminotransferase; Provisional; Region: PRK06082 998088005383 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 998088005384 inhibitor-cofactor binding pocket; inhibition site 998088005385 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088005386 catalytic residue [active] 998088005387 phosphonoacetaldehyde hydrolase; Provisional; Region: PRK13478 998088005388 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 998088005389 motif II; other site 998088005390 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_36; cd04695 998088005391 nudix motif; other site 998088005392 Predicted Zn-dependent protease (DUF2268); Region: DUF2268; cl02316 998088005393 cytochrome c nitrite reductase, accessory protein NrfF; Region: cyt_nit_nrfF; TIGR03147 998088005394 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 998088005395 binding surface 998088005396 TPR motif; other site 998088005397 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 998088005398 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 998088005399 catalytic residues [active] 998088005400 central insert; other site 998088005401 cytochrome c nitrate reductase biogenesis protein NrfE; Region: cyt_nit_nrfE; TIGR03145 998088005402 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 998088005403 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 998088005404 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 998088005405 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 998088005406 cytochrome c nitrite reductase, pentaheme subunit; Region: cyt_nit_nrfB; TIGR03146 998088005407 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 998088005408 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 998088005409 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088005410 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088005411 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088005412 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088005413 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088005414 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088005415 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088005416 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 998088005417 glycerol-3-phosphate dehydrogenase, anaerobic, C subunit; Region: glycerol3P_GlpC; TIGR03379 998088005418 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 998088005419 Cysteine-rich domain; Region: CCG; pfam02754 998088005420 Cysteine-rich domain; Region: CCG; pfam02754 998088005421 anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated; Region: PRK05329 998088005422 glycerol-3-phosphate dehydrogenase, anaerobic, B subunit; Region: glycerol3P_GlpB; TIGR03378 998088005423 sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional; Region: glpA; PRK11101 998088005424 hydroxyglutarate oxidase; Provisional; Region: PRK11728 998088005425 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 998088005426 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 998088005427 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 998088005428 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 998088005429 dimerization interface [polypeptide binding]; other site 998088005430 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088005431 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088005432 dimer interface [polypeptide binding]; other site 998088005433 putative CheW interface [polypeptide binding]; other site 998088005434 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 998088005435 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 998088005436 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 998088005437 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 998088005438 Uncharacterized conserved protein [Function unknown]; Region: COG3148 998088005439 hypothetical protein; Provisional; Region: PRK10621 998088005440 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 998088005441 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088005442 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088005443 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 998088005444 dimerization interface [polypeptide binding]; other site 998088005445 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088005446 EamA-like transporter family; Region: EamA; pfam00892 998088005447 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088005448 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088005449 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088005450 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 998088005451 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 998088005452 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 998088005453 putative active site [active] 998088005454 putative metal-binding site [ion binding]; other site 998088005455 Type II secretory pathway, pullulanase PulA and related glycosidases [Carbohydrate transport and metabolism]; Region: PulA; COG1523 998088005456 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 998088005457 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 998088005458 active site 998088005459 catalytic site [active] 998088005460 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 998088005461 interface (dimer of trimers) [polypeptide binding]; other site 998088005462 Substrate-binding/catalytic site; other site 998088005463 Zn-binding sites [ion binding]; other site 998088005464 dUMP phosphatase; Provisional; Region: PRK09449 998088005465 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 998088005466 motif II; other site 998088005467 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088005468 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 998088005469 substrate binding pocket [chemical binding]; other site 998088005470 membrane-bound complex binding site; other site 998088005471 hinge residues; other site 998088005472 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 998088005473 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 998088005474 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 998088005475 FMN binding site [chemical binding]; other site 998088005476 active site 998088005477 catalytic residues [active] 998088005478 substrate binding site [chemical binding]; other site 998088005479 Protein of unknown function (DUF454); Region: DUF454; cl01063 998088005480 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 998088005481 active site 998088005482 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 998088005483 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 998088005484 Walker A motif; other site 998088005485 ATP binding site [chemical binding]; other site 998088005486 Walker B motif; other site 998088005487 DNA polymerase III subunit delta'; Validated; Region: PRK08485 998088005488 arginine finger; other site 998088005489 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 998088005490 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 998088005491 hypothetical protein; Validated; Region: PRK00153 998088005492 endonuclease IV; Provisional; Region: PRK01060 998088005493 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 998088005494 AP (apurinic/apyrimidinic) site pocket; other site 998088005495 DNA interaction; other site 998088005496 Metal-binding active site; metal-binding site 998088005497 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 998088005498 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088005499 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 998088005500 putative dimerization interface [polypeptide binding]; other site 998088005501 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 998088005502 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 998088005503 gating phenylalanine in ion channel; other site 998088005504 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 998088005505 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 998088005506 putative acyl-acceptor binding pocket; other site 998088005507 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 998088005508 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 998088005509 putative acyl-acceptor binding pocket; other site 998088005510 Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning]; Region: RIO1; COG1718 998088005511 RIO kinase family; RIO1, RIO3 and similar proteins, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein...; Region: RIO1_like; cd05145 998088005512 ATP binding site [chemical binding]; other site 998088005513 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 998088005514 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088005515 Coenzyme A binding pocket [chemical binding]; other site 998088005516 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088005517 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088005518 metal binding site [ion binding]; metal-binding site 998088005519 active site 998088005520 I-site; other site 998088005521 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 998088005522 putative deacylase active site [active] 998088005523 DNA polymerase II; Reviewed; Region: PRK05762 998088005524 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 998088005525 active site 998088005526 catalytic site [active] 998088005527 substrate binding site [chemical binding]; other site 998088005528 DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as...; Region: POLBc_Pol_II; cd05537 998088005529 active site 998088005530 metal-binding site 998088005531 DinI-like family; Region: DinI; cl11630 998088005532 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 998088005533 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 998088005534 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 998088005535 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 998088005536 active site 998088005537 metal binding site [ion binding]; metal-binding site 998088005538 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 998088005539 C4-dicarboxylate transporter DcuC; Provisional; Region: dcuC; PRK10654 998088005540 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 998088005541 Bacterial protein of unknown function (DUF922); Region: DUF922; cl02415 998088005542 Uncharacterized conserved protein [Function unknown]; Region: COG4121 998088005543 tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain; Region: MnmC_Cterm; TIGR03197 998088005544 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088005545 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 998088005546 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 998088005547 dimer interface [polypeptide binding]; other site 998088005548 active site 998088005549 putative transporter; Provisional; Region: PRK04972 998088005550 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 998088005551 TrkA-C domain; Region: TrkA_C; pfam02080 998088005552 TrkA-C domain; Region: TrkA_C; pfam02080 998088005553 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 998088005554 excinuclease ABC subunit B; Provisional; Region: PRK05298 998088005555 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 998088005556 ATP binding site [chemical binding]; other site 998088005557 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 998088005558 nucleotide binding region [chemical binding]; other site 998088005559 ATP-binding site [chemical binding]; other site 998088005560 Ultra-violet resistance protein B; Region: UvrB; pfam12344 998088005561 UvrB/uvrC motif; Region: UVR; pfam02151 998088005562 Uncharacterized conserved protein [Function unknown]; Region: COG3339 998088005563 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 998088005564 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 998088005565 disulfide bond formation protein B; Provisional; Region: PRK01749 998088005566 sodium/proton antiporter; Reviewed; Region: nhaB; PRK09547 998088005567 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 998088005568 fatty acid metabolism regulator; Provisional; Region: PRK04984 998088005569 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088005570 DNA-binding site [nucleotide binding]; DNA binding site 998088005571 FadR C-terminal domain; Region: FadR_C; pfam07840 998088005572 TIGR02808 family protein; Region: short_TIGR02808 998088005573 YaeQ protein; Region: YaeQ; pfam07152 998088005574 Membrane transport protein; Region: Mem_trans; cl09117 998088005575 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 998088005576 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 998088005577 non-specific DNA binding site [nucleotide binding]; other site 998088005578 salt bridge; other site 998088005579 sequence-specific DNA binding site [nucleotide binding]; other site 998088005580 Predicted transcriptional regulator [Transcription]; Region: COG2932 998088005581 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 998088005582 Catalytic site [active] 998088005583 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 998088005584 Integrase core domain; Region: rve; pfam00665 998088005585 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 998088005586 AAA ATPase domain; Region: AAA_16; pfam13191 998088005587 AAA domain; Region: AAA_22; pfam13401 998088005588 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 998088005589 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 998088005590 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 998088005591 Uncharacterized conserved protein [Function unknown]; Region: COG5566 998088005592 Glycosyl hydrolase 108; Region: Glyco_hydro_108; pfam05838 998088005593 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 998088005594 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 998088005595 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 998088005596 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 998088005597 Protein of unknown function (DUF935); Region: DUF935; pfam06074 998088005598 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 998088005599 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 998088005600 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 998088005601 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 998088005602 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; pfam10124 998088005603 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 998088005604 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 998088005605 Uncharacterized protein family (UPF0157); Region: UPF0157; cl00987 998088005606 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 998088005607 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 998088005608 binding surface 998088005609 TPR motif; other site 998088005610 tape measure domain; Region: tape_meas_nterm; TIGR02675 998088005611 Membrane transport protein; Region: Mem_trans; cl09117 998088005612 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 998088005613 GAF domain; Region: GAF; cl17456 998088005614 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 998088005615 Walker A motif; other site 998088005616 ATP binding site [chemical binding]; other site 998088005617 Walker B motif; other site 998088005618 arginine finger; other site 998088005619 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 998088005620 multidrug efflux protein; Reviewed; Region: PRK01766 998088005621 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 998088005622 cation binding site [ion binding]; other site 998088005623 hypothetical protein; Provisional; Region: PRK04964 998088005624 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088005625 EamA-like transporter family; Region: EamA; pfam00892 998088005626 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 998088005627 Lumazine binding domain; Region: Lum_binding; pfam00677 998088005628 Lumazine binding domain; Region: Lum_binding; pfam00677 998088005629 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 998088005630 2-deoxyglucose-6-phosphatase; Provisional; Region: PRK10826 998088005631 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 998088005632 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 998088005633 motif II; other site 998088005634 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 998088005635 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088005636 ATP-grasp domain; Region: ATP-grasp; pfam02222 998088005637 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088005638 azoreductase; Reviewed; Region: PRK00170 998088005639 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 998088005640 Domain of unknown function (DUF4250); Region: DUF4250; pfam14056 998088005641 Transcriptional regulators [Transcription]; Region: MarR; COG1846 998088005642 MarR family; Region: MarR_2; pfam12802 998088005643 Uncharacterized protein family (UPF0149); Region: UPF0149; pfam03695 998088005644 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 998088005645 S1 domain; Region: S1_2; pfam13509 998088005646 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 998088005647 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 998088005648 Protein of unknown function, DUF440; Region: DUF440; cl11472 998088005649 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 998088005650 Transglycosylase; Region: Transgly; cl17702 998088005651 Protein of unknown function, DUF440; Region: DUF440; pfam04269 998088005652 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 998088005653 cell division inhibitor MinD; Provisional; Region: PRK10818 998088005654 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 998088005655 Switch I; other site 998088005656 Switch II; other site 998088005657 septum formation inhibitor; Reviewed; Region: minC; PRK04804 998088005658 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 998088005659 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 998088005660 YcgL domain; Region: YcgL; pfam05166 998088005661 Integrase core domain; Region: rve_3; pfam13683 998088005662 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 998088005663 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 998088005664 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 998088005665 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 998088005666 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 998088005667 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 998088005668 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 998088005669 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 998088005670 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 998088005671 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent...; Region: Bacterial_PFK; cd00763 998088005672 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 998088005673 active site 998088005674 ADP/pyrophosphate binding site [chemical binding]; other site 998088005675 dimerization interface [polypeptide binding]; other site 998088005676 allosteric effector site; other site 998088005677 fructose-1,6-bisphosphate binding site; other site 998088005678 triosephosphate isomerase; Provisional; Region: PRK14567 998088005679 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 998088005680 substrate binding site [chemical binding]; other site 998088005681 dimer interface [polypeptide binding]; other site 998088005682 catalytic triad [active] 998088005683 Uncharacterized conserved protein [Function unknown]; Region: COG1434 998088005684 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 998088005685 putative active site [active] 998088005686 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 998088005687 S-adenosylmethionine binding site [chemical binding]; other site 998088005688 condesin subunit F; Provisional; Region: PRK05260 998088005689 condesin subunit E; Provisional; Region: PRK05256 998088005690 cell division protein MukB; Provisional; Region: mukB; PRK04863 998088005691 P-loop containing region of AAA domain; Region: AAA_29; cl17516 998088005692 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 998088005693 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 998088005694 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 998088005695 nitrobindin heme-binding domain; Region: nitrobindin; cl10502 998088005696 heme-binding site [chemical binding]; other site 998088005697 PGAP1-like protein; Region: PGAP1; pfam07819 998088005698 Uncharacterized protein conserved in bacteria C-term(DUF2220); Region: DUF2220; pfam09983 998088005699 aspartate/ornithine carbamoyltransferase family protein; Validated; Region: PRK07200 998088005700 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 998088005701 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 998088005702 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 998088005703 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; cd00640 998088005704 catalytic residue [active] 998088005705 peptidase; Reviewed; Region: PRK13004 998088005706 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like4; cd05649 998088005707 putative metal binding site [ion binding]; other site 998088005708 putative dimer interface [polypeptide binding]; other site 998088005709 phenylhydantoinase; Validated; Region: PRK08323 998088005710 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 998088005711 tetramer interface [polypeptide binding]; other site 998088005712 active site 998088005713 carbamate kinase; Reviewed; Region: PRK12686 998088005714 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 998088005715 putative substrate binding site [chemical binding]; other site 998088005716 homodimer interface [polypeptide binding]; other site 998088005717 nucleotide binding site [chemical binding]; other site 998088005718 nucleotide binding site [chemical binding]; other site 998088005719 EamA-like transporter family; Region: EamA; pfam00892 998088005720 EamA-like transporter family; Region: EamA; pfam00892 998088005721 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 998088005722 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 998088005723 XdhC Rossmann domain; Region: XdhC_C; pfam13478 998088005724 selenium-dependent molybdenum hydroxylase system protein, YqeB family; Region: matur_yqeB; TIGR03309 998088005725 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 998088005726 probable selenium-dependent hydroxylase accessory protein YqeC; Region: TIGR03172 998088005727 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 998088005728 metal-binding site 998088005729 putative selenate reductase subunit YgfK; Provisional; Region: PRK09853 998088005730 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 998088005731 phosphate binding site [ion binding]; other site 998088005732 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 998088005733 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088005734 putative selenium metabolism protein SsnA; Region: Se_ssnA; TIGR03314 998088005735 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 998088005736 active site 998088005737 putative substrate binding pocket [chemical binding]; other site 998088005738 probable selenate reductase, FAD-binding subunit; Region: Se_sel_red_FAD; TIGR03312 998088005739 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 998088005740 putative hypoxanthine oxidase; Provisional; Region: PRK09800 998088005741 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 998088005742 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 998088005743 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 998088005744 xanthine permease; Region: pbuX; TIGR03173 998088005745 guanine deaminase; Provisional; Region: PRK09228 998088005746 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 998088005747 active site 998088005748 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 998088005749 xanthine dehydrogenase subunit XdhA; Provisional; Region: PRK09970 998088005750 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 998088005751 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 998088005752 xanthine dehydrogenase subunit XdhB; Provisional; Region: PRK09971 998088005753 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 998088005754 xanthine dehydrogenase subunit XdhC; Provisional; Region: PRK09908 998088005755 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 998088005756 catalytic loop [active] 998088005757 iron binding site [ion binding]; other site 998088005758 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 998088005759 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 998088005760 HTH-like domain; Region: HTH_21; pfam13276 998088005761 Integrase core domain; Region: rve; pfam00665 998088005762 Integrase core domain; Region: rve_3; pfam13683 998088005763 hypothetical protein; Provisional; Region: PRK11280 998088005764 acyl-CoA synthetase; Validated; Region: PRK08162 998088005765 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 998088005766 acyl-activating enzyme (AAE) consensus motif; other site 998088005767 putative active site [active] 998088005768 AMP binding site [chemical binding]; other site 998088005769 putative CoA binding site [chemical binding]; other site 998088005770 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 998088005771 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 998088005772 putative active site [active] 998088005773 heme pocket [chemical binding]; other site 998088005774 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 998088005775 putative active site [active] 998088005776 heme pocket [chemical binding]; other site 998088005777 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088005778 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088005779 metal binding site [ion binding]; metal-binding site 998088005780 active site 998088005781 I-site; other site 998088005782 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 998088005783 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 998088005784 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 998088005785 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 998088005786 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 998088005787 metal binding site [ion binding]; metal-binding site 998088005788 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 998088005789 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 998088005790 substrate binding site [chemical binding]; other site 998088005791 glutamase interaction surface [polypeptide binding]; other site 998088005792 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 998088005793 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 998088005794 catalytic residues [active] 998088005795 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 998088005796 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 998088005797 putative active site [active] 998088005798 oxyanion strand; other site 998088005799 catalytic triad [active] 998088005800 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 998088005801 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 998088005802 active site 998088005803 motif I; other site 998088005804 motif II; other site 998088005805 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 998088005806 putative active site pocket [active] 998088005807 4-fold oligomerization interface [polypeptide binding]; other site 998088005808 metal binding residues [ion binding]; metal-binding site 998088005809 3-fold/trimer interface [polypeptide binding]; other site 998088005810 histidinol-phosphate aminotransferase; Provisional; Region: PRK01688 998088005811 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 998088005812 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088005813 homodimer interface [polypeptide binding]; other site 998088005814 catalytic residue [active] 998088005815 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 998088005816 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 998088005817 NAD binding site [chemical binding]; other site 998088005818 dimerization interface [polypeptide binding]; other site 998088005819 product binding site; other site 998088005820 substrate binding site [chemical binding]; other site 998088005821 zinc binding site [ion binding]; other site 998088005822 catalytic residues [active] 998088005823 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 998088005824 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 998088005825 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 998088005826 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 998088005827 DEAD/DEAH box helicase; Region: DEAD; pfam00270 998088005828 ATP binding site [chemical binding]; other site 998088005829 DEAD_2; Region: DEAD_2; pfam06733 998088005830 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 998088005831 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 998088005832 Glycoprotease family; Region: Peptidase_M22; pfam00814 998088005833 Outer membrane lipoprotein Slp family; Region: Slp; pfam03843 998088005834 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 998088005835 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 998088005836 nucleophilic elbow; other site 998088005837 catalytic triad; other site 998088005838 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 998088005839 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 998088005840 acyl-activating enzyme (AAE) consensus motif; other site 998088005841 putative AMP binding site [chemical binding]; other site 998088005842 putative active site [active] 998088005843 putative CoA binding site [chemical binding]; other site 998088005844 ribonuclease D; Provisional; Region: PRK10829 998088005845 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 998088005846 catalytic site [active] 998088005847 putative active site [active] 998088005848 putative substrate binding site [chemical binding]; other site 998088005849 HRDC domain; Region: HRDC; pfam00570 998088005850 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 998088005851 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 998088005852 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 998088005853 active site residue [active] 998088005854 selenophosphate synthetase; Provisional; Region: PRK00943 998088005855 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 998088005856 dimerization interface [polypeptide binding]; other site 998088005857 putative ATP binding site [chemical binding]; other site 998088005858 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088005859 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 998088005860 Coenzyme A binding pocket [chemical binding]; other site 998088005861 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 998088005862 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 998088005863 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 998088005864 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 998088005865 putative RNA binding site [nucleotide binding]; other site 998088005866 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 998088005867 S-adenosylmethionine binding site [chemical binding]; other site 998088005868 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088005869 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088005870 dimer interface [polypeptide binding]; other site 998088005871 putative CheW interface [polypeptide binding]; other site 998088005872 Acylphosphatase; Region: Acylphosphatase; pfam00708 998088005873 CHAD domain; Region: CHAD; pfam05235 998088005874 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 998088005875 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 998088005876 active site 998088005877 HIGH motif; other site 998088005878 KMSKS motif; other site 998088005879 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 998088005880 tRNA binding surface [nucleotide binding]; other site 998088005881 anticodon binding site; other site 998088005882 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 998088005883 dimer interface [polypeptide binding]; other site 998088005884 putative tRNA-binding site [nucleotide binding]; other site 998088005885 antiporter inner membrane protein; Provisional; Region: PRK11670 998088005886 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 998088005887 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 998088005888 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 998088005889 ATP-binding site [chemical binding]; other site 998088005890 Sugar specificity; other site 998088005891 Pyrimidine base specificity; other site 998088005892 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 998088005893 trimer interface [polypeptide binding]; other site 998088005894 active site 998088005895 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 998088005896 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 998088005897 Predicted Fe-S protein [General function prediction only]; Region: COG3313 998088005898 murein transglycosylase A; Provisional; Region: mltA; PRK11162 998088005899 MltA specific insert domain; Region: MltA; smart00925 998088005900 3D domain; Region: 3D; pfam06725 998088005901 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 998088005902 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 998088005903 catalytic loop [active] 998088005904 iron binding site [ion binding]; other site 998088005905 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 998088005906 dimer interface [polypeptide binding]; other site 998088005907 putative radical transfer pathway; other site 998088005908 diiron center [ion binding]; other site 998088005909 tyrosyl radical; other site 998088005910 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 998088005911 ATP cone domain; Region: ATP-cone; pfam03477 998088005912 Class I ribonucleotide reductase; Region: RNR_I; cd01679 998088005913 active site 998088005914 dimer interface [polypeptide binding]; other site 998088005915 catalytic residues [active] 998088005916 effector binding site; other site 998088005917 R2 peptide binding site; other site 998088005918 phosphoglycolate phosphatase; Provisional; Region: PRK13222 998088005919 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 998088005920 motif II; other site 998088005921 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 998088005922 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 998088005923 S-adenosylmethionine binding site [chemical binding]; other site 998088005924 DNA gyrase subunit A; Validated; Region: PRK05560 998088005925 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 998088005926 CAP-like domain; other site 998088005927 active site 998088005928 primary dimer interface [polypeptide binding]; other site 998088005929 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005930 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005931 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005932 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005933 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005934 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 998088005935 Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac1_AmyA; cd11315 998088005936 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 998088005937 active site 998088005938 Ca binding site [ion binding]; other site 998088005939 catalytic site [active] 998088005940 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 998088005941 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 998088005942 FeS/SAM binding site; other site 998088005943 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 998088005944 Sel1-like repeats; Region: SEL1; smart00671 998088005945 Sel1-like repeats; Region: SEL1; smart00671 998088005946 Sel1 repeat; Region: Sel1; cl02723 998088005947 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 998088005948 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 998088005949 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 998088005950 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 998088005951 active site 998088005952 dimer interface [polypeptide binding]; other site 998088005953 motif 1; other site 998088005954 motif 2; other site 998088005955 motif 3; other site 998088005956 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 998088005957 anticodon binding site; other site 998088005958 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 998088005959 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 998088005960 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 998088005961 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 998088005962 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 998088005963 23S rRNA binding site [nucleotide binding]; other site 998088005964 L21 binding site [polypeptide binding]; other site 998088005965 L13 binding site [polypeptide binding]; other site 998088005966 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 998088005967 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 998088005968 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 998088005969 dimer interface [polypeptide binding]; other site 998088005970 motif 1; other site 998088005971 active site 998088005972 motif 2; other site 998088005973 motif 3; other site 998088005974 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 998088005975 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 998088005976 putative tRNA-binding site [nucleotide binding]; other site 998088005977 B3/4 domain; Region: B3_4; pfam03483 998088005978 tRNA synthetase B5 domain; Region: B5; smart00874 998088005979 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 998088005980 dimer interface [polypeptide binding]; other site 998088005981 motif 1; other site 998088005982 motif 3; other site 998088005983 motif 2; other site 998088005984 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 998088005985 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 998088005986 IHF dimer interface [polypeptide binding]; other site 998088005987 IHF - DNA interface [nucleotide binding]; other site 998088005988 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 998088005989 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 998088005990 substrate binding pocket [chemical binding]; other site 998088005991 membrane-bound complex binding site; other site 998088005992 hinge residues; other site 998088005993 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 998088005994 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088005995 substrate binding pocket [chemical binding]; other site 998088005996 membrane-bound complex binding site; other site 998088005997 hinge residues; other site 998088005998 PAS fold; Region: PAS_3; pfam08447 998088005999 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 998088006000 dimer interface [polypeptide binding]; other site 998088006001 phosphorylation site [posttranslational modification] 998088006002 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 998088006003 ATP binding site [chemical binding]; other site 998088006004 Mg2+ binding site [ion binding]; other site 998088006005 G-X-G motif; other site 998088006006 Response regulator receiver domain; Region: Response_reg; pfam00072 998088006007 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 998088006008 active site 998088006009 phosphorylation site [posttranslational modification] 998088006010 intermolecular recognition site; other site 998088006011 dimerization interface [polypeptide binding]; other site 998088006012 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 998088006013 putative binding surface; other site 998088006014 active site 998088006015 Response regulator receiver domain; Region: Response_reg; pfam00072 998088006016 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 998088006017 active site 998088006018 phosphorylation site [posttranslational modification] 998088006019 intermolecular recognition site; other site 998088006020 dimerization interface [polypeptide binding]; other site 998088006021 NAD-dependent deacetylase; Provisional; Region: PRK00481 998088006022 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 998088006023 NAD+ binding site [chemical binding]; other site 998088006024 substrate binding site [chemical binding]; other site 998088006025 Zn binding site [ion binding]; other site 998088006026 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 998088006027 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088006028 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006029 metal binding site [ion binding]; metal-binding site 998088006030 active site 998088006031 I-site; other site 998088006032 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 998088006033 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088006034 DNA binding site [nucleotide binding] 998088006035 domain linker motif; other site 998088006036 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 998088006037 dimerization interface [polypeptide binding]; other site 998088006038 ligand binding site [chemical binding]; other site 998088006039 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 998088006040 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 998088006041 substrate binding site [chemical binding]; other site 998088006042 dimer interface [polypeptide binding]; other site 998088006043 ATP binding site [chemical binding]; other site 998088006044 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 998088006045 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 998088006046 ligand binding site [chemical binding]; other site 998088006047 dimerization interface [polypeptide binding]; other site 998088006048 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 998088006049 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 998088006050 TM-ABC transporter signature motif; other site 998088006051 D-ribose transporter ATP binding protein; Provisional; Region: PRK10762 998088006052 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 998088006053 Walker A/P-loop; other site 998088006054 ATP binding site [chemical binding]; other site 998088006055 Q-loop/lid; other site 998088006056 ABC transporter signature motif; other site 998088006057 Walker B; other site 998088006058 D-loop; other site 998088006059 H-loop/switch region; other site 998088006060 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 998088006061 D-ribose pyranase; Provisional; Region: PRK11797 998088006062 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 998088006063 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 998088006064 C-terminal domain interface [polypeptide binding]; other site 998088006065 GSH binding site (G-site) [chemical binding]; other site 998088006066 dimer interface [polypeptide binding]; other site 998088006067 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 998088006068 dimer interface [polypeptide binding]; other site 998088006069 substrate binding pocket (H-site) [chemical binding]; other site 998088006070 N-terminal domain interface [polypeptide binding]; other site 998088006071 spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed; Region: potD; PRK09501 998088006072 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 998088006073 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 998088006074 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 998088006075 dimer interface [polypeptide binding]; other site 998088006076 conserved gate region; other site 998088006077 ABC-ATPase subunit interface; other site 998088006078 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 998088006079 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 998088006080 dimer interface [polypeptide binding]; other site 998088006081 conserved gate region; other site 998088006082 putative PBP binding loops; other site 998088006083 ABC-ATPase subunit interface; other site 998088006084 putrescine/spermidine ABC transporter ATPase protein; Reviewed; Region: potA; PRK09452 998088006085 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088006086 Walker A/P-loop; other site 998088006087 ATP binding site [chemical binding]; other site 998088006088 Q-loop/lid; other site 998088006089 ABC transporter signature motif; other site 998088006090 Walker B; other site 998088006091 D-loop; other site 998088006092 H-loop/switch region; other site 998088006093 TOBE domain; Region: TOBE_2; pfam08402 998088006094 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 998088006095 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 998088006096 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 998088006097 Ligand Binding Site [chemical binding]; other site 998088006098 universal stress protein UspE; Provisional; Region: PRK11175 998088006099 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 998088006100 Ligand Binding Site [chemical binding]; other site 998088006101 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 998088006102 Ligand Binding Site [chemical binding]; other site 998088006103 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 998088006104 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 998088006105 ligand binding site [chemical binding]; other site 998088006106 flexible hinge region; other site 998088006107 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 998088006108 putative switch regulator; other site 998088006109 non-specific DNA interactions [nucleotide binding]; other site 998088006110 DNA binding site [nucleotide binding] 998088006111 sequence specific DNA binding site [nucleotide binding]; other site 998088006112 putative cAMP binding site [chemical binding]; other site 998088006113 Family description; Region: DsbD_2; pfam13386 998088006114 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 998088006115 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 998088006116 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 998088006117 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 998088006118 metal-binding site [ion binding] 998088006119 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 998088006120 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 998088006121 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 998088006122 FixH; Region: FixH; pfam05751 998088006123 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 998088006124 Cytochrome c; Region: Cytochrom_C; pfam00034 998088006125 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 998088006126 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 998088006127 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 998088006128 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 998088006129 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 998088006130 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 998088006131 Low-spin heme binding site [chemical binding]; other site 998088006132 Putative water exit pathway; other site 998088006133 Binuclear center (active site) [active] 998088006134 Putative proton exit pathway; other site 998088006135 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 998088006136 GAF domain; Region: GAF_2; pfam13185 998088006137 ProP expression regulator; Provisional; Region: PRK04950 998088006138 ProQ/FINO family; Region: ProQ; pfam04352 998088006139 carboxy-terminal protease; Provisional; Region: PRK11186 998088006140 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 998088006141 protein binding site [polypeptide binding]; other site 998088006142 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 998088006143 Catalytic dyad [active] 998088006144 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 998088006145 aminopeptidase N; Provisional; Region: pepN; PRK14015 998088006146 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 998088006147 active site 998088006148 Zn binding site [ion binding]; other site 998088006149 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 998088006150 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 998088006151 ATP P2X receptor; Region: P2X_receptor; cl02993 998088006152 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 998088006153 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 998088006154 quinone interaction residues [chemical binding]; other site 998088006155 active site 998088006156 catalytic residues [active] 998088006157 FMN binding site [chemical binding]; other site 998088006158 substrate binding site [chemical binding]; other site 998088006159 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 998088006160 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 998088006161 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 998088006162 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 998088006163 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 998088006164 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 998088006165 S-adenosylmethionine binding site [chemical binding]; other site 998088006166 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 998088006167 ABC transporter ATPase component; Reviewed; Region: PRK11147 998088006168 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088006169 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088006170 ABC transporter; Region: ABC_tran_2; pfam12848 998088006171 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088006172 Ribosome modulation factor; Region: RMF; pfam04957 998088006173 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 998088006174 active site 1 [active] 998088006175 dimer interface [polypeptide binding]; other site 998088006176 active site 2 [active] 998088006177 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 998088006178 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 998088006179 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 998088006180 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 998088006181 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 998088006182 INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in...; Region: INT_SG1_C; cd01183 998088006183 Int/Topo IB signature motif; other site 998088006184 YebG protein; Region: YebG; pfam07130 998088006185 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088006186 PGAP1-like protein; Region: PGAP1; pfam07819 998088006187 short chain dehydrogenase; Provisional; Region: PRK07201 998088006188 Pseudomonas fluorescens MupV-like, extended (e) SDRs; Region: MupV_like_SDR_e; cd05263 998088006189 putative NAD(P) binding site [chemical binding]; other site 998088006190 active site 998088006191 putative substrate binding site [chemical binding]; other site 998088006192 classical (c) SDRs; Region: SDR_c; cd05233 998088006193 NAD(P) binding site [chemical binding]; other site 998088006194 active site 998088006195 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; pfam05597 998088006196 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 998088006197 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088006198 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088006199 Bacterial transcriptional repressor; Region: TetR; pfam13972 998088006200 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 998088006201 binding surface 998088006202 TPR motif; other site 998088006203 acyltransferase, WS/DGAT/MGAT; Region: acyl_WS_DGAT; TIGR02946 998088006204 Wax ester synthase-like Acyl-CoA acyltransferase domain; Region: WES_acyltransf; pfam03007 998088006205 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; cl09865 998088006206 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 998088006207 2-methylcitrate dehydratase; Region: prpD; TIGR02330 998088006208 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A; Region: CS_ACL-C_CCL; cl00416 998088006209 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 998088006210 oxalacetate binding site [chemical binding]; other site 998088006211 citrylCoA binding site [chemical binding]; other site 998088006212 coenzyme A binding site [chemical binding]; other site 998088006213 catalytic triad [active] 998088006214 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 998088006215 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 998088006216 tetramer interface [polypeptide binding]; other site 998088006217 active site 998088006218 Mg2+/Mn2+ binding site [ion binding]; other site 998088006219 Paraquat-inducible protein A; Region: PqiA; pfam04403 998088006220 Paraquat-inducible protein A; Region: PqiA; pfam04403 998088006221 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 998088006222 mce related protein; Region: MCE; pfam02470 998088006223 mce related protein; Region: MCE; pfam02470 998088006224 mce related protein; Region: MCE; pfam02470 998088006225 mce related protein; Region: MCE; pfam02470 998088006226 mce related protein; Region: MCE; pfam02470 998088006227 mce related protein; Region: MCE; pfam02470 998088006228 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 998088006229 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 998088006230 S-adenosylmethionine binding site [chemical binding]; other site 998088006231 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 998088006232 Replication regulatory protein RepB; Region: RepB-RCR_reg; cl11673 998088006233 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 998088006234 active site 998088006235 DNA binding site [nucleotide binding] 998088006236 Int/Topo IB signature motif; other site 998088006237 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 998088006238 active site 998088006239 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 998088006240 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 998088006241 Walker A motif; other site 998088006242 ATP binding site [chemical binding]; other site 998088006243 Walker B motif; other site 998088006244 ATPase involved in DNA replication [DNA replication, recombination, and repair]; Region: HolB; COG0470 998088006245 arginine finger; other site 998088006246 DNA polymerase III, delta subunit, C terminal; Region: DNApol3-delta_C; pfam09115 998088006247 thymidylate kinase; Validated; Region: tmk; PRK00698 998088006248 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 998088006249 TMP-binding site; other site 998088006250 ATP-binding site [chemical binding]; other site 998088006251 YceG-like family; Region: YceG; pfam02618 998088006252 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 998088006253 dimerization interface [polypeptide binding]; other site 998088006254 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 998088006255 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 998088006256 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088006257 catalytic residue [active] 998088006258 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 998088006259 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 998088006260 dimer interface [polypeptide binding]; other site 998088006261 active site 998088006262 acyl carrier protein; Provisional; Region: acpP; PRK00982 998088006263 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 998088006264 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 998088006265 NAD(P) binding site [chemical binding]; other site 998088006266 homotetramer interface [polypeptide binding]; other site 998088006267 homodimer interface [polypeptide binding]; other site 998088006268 active site 998088006269 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 998088006270 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 998088006271 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 998088006272 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 998088006273 dimer interface [polypeptide binding]; other site 998088006274 active site 998088006275 CoA binding pocket [chemical binding]; other site 998088006276 putative phosphate acyltransferase; Provisional; Region: PRK05331 998088006277 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 998088006278 hypothetical protein; Provisional; Region: PRK11193 998088006279 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 998088006280 active site 998088006281 dimer interface [polypeptide binding]; other site 998088006282 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 998088006283 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 998088006284 motif II; other site 998088006285 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 998088006286 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 998088006287 RNA binding surface [nucleotide binding]; other site 998088006288 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 998088006289 active site 998088006290 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 998088006291 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 998088006292 homodimer interface [polypeptide binding]; other site 998088006293 oligonucleotide binding site [chemical binding]; other site 998088006294 PTS system fructose-specific transporter subunits IIBC; Provisional; Region: PRK10712 998088006295 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 998088006296 active site 998088006297 P-loop; other site 998088006298 phosphorylation site [posttranslational modification] 998088006299 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 998088006300 active site 998088006301 P-loop; other site 998088006302 phosphorylation site [posttranslational modification] 998088006303 PTS system, fructose subfamily, IIC component; Region: PTS_IIC_fructo; TIGR01427 998088006304 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 998088006305 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 998088006306 putative substrate binding site [chemical binding]; other site 998088006307 putative ATP binding site [chemical binding]; other site 998088006308 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional; Region: PRK11109 998088006309 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 998088006310 active site 998088006311 phosphorylation site [posttranslational modification] 998088006312 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 998088006313 dimerization domain swap beta strand [polypeptide binding]; other site 998088006314 regulatory protein interface [polypeptide binding]; other site 998088006315 active site 998088006316 regulatory phosphorylation site [posttranslational modification]; other site 998088006317 DNA-binding transcriptional regulator FruR; Provisional; Region: PRK11303 998088006318 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088006319 DNA binding site [nucleotide binding] 998088006320 domain linker motif; other site 998088006321 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 998088006322 dimerization interface [polypeptide binding]; other site 998088006323 ligand binding site [chemical binding]; other site 998088006324 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 998088006325 aromatic amino acid transport protein; Region: araaP; TIGR00837 998088006326 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4337 998088006327 MAPEG family; Region: MAPEG; cl09190 998088006328 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 998088006329 DEAD-like helicases superfamily; Region: DEXDc; smart00487 998088006330 ATP binding site [chemical binding]; other site 998088006331 Mg++ binding site [ion binding]; other site 998088006332 motif III; other site 998088006333 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 998088006334 nucleotide binding region [chemical binding]; other site 998088006335 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088006336 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 998088006337 substrate binding pocket [chemical binding]; other site 998088006338 hinge residues; other site 998088006339 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 998088006340 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 998088006341 Tetramer interface [polypeptide binding]; other site 998088006342 active site 998088006343 FMN-binding site [chemical binding]; other site 998088006344 HemK family putative methylases; Region: hemK_fam; TIGR00536 998088006345 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 998088006346 S-adenosylmethionine binding site [chemical binding]; other site 998088006347 hypothetical protein; Provisional; Region: PRK04946 998088006348 Smr domain; Region: Smr; pfam01713 998088006349 PAS domain; Region: PAS_9; pfam13426 998088006350 PAS domain S-box; Region: sensory_box; TIGR00229 998088006351 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 998088006352 putative active site [active] 998088006353 heme pocket [chemical binding]; other site 998088006354 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088006355 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006356 metal binding site [ion binding]; metal-binding site 998088006357 active site 998088006358 I-site; other site 998088006359 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 998088006360 catalytic core [active] 998088006361 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 998088006362 Glycoside hydrolase family 19 chitinase domain. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Family 19 chitinases are found primarily in plants (classes I, III, and IV), but some...; Region: chitinase_glyco_hydro_19; cd00325 998088006363 putative sugar binding site [chemical binding]; other site 998088006364 catalytic residues [active] 998088006365 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088006366 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088006367 Methyltransferase domain; Region: Methyltransf_32; pfam13679 998088006368 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 998088006369 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 998088006370 PhnA protein; Region: PhnA; pfam03831 998088006371 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 998088006372 Fumarase C-terminus; Region: Fumerase_C; pfam05683 998088006373 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 998088006374 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 998088006375 chorismate binding enzyme; Region: Chorismate_bind; cl10555 998088006376 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 998088006377 putative active site [active] 998088006378 putative CoA binding site [chemical binding]; other site 998088006379 nudix motif; other site 998088006380 metal binding site [ion binding]; metal-binding site 998088006381 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088006382 serine transporter; Region: stp; TIGR00814 998088006383 serine/threonine transporter SstT; Provisional; Region: PRK13628 998088006384 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 998088006385 DEAD-like helicases superfamily; Region: DEXDc; smart00487 998088006386 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 998088006387 ATP binding site [chemical binding]; other site 998088006388 putative Mg++ binding site [ion binding]; other site 998088006389 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 998088006390 nucleotide binding region [chemical binding]; other site 998088006391 ATP-binding site [chemical binding]; other site 998088006392 PrkA family serine protein kinase; Provisional; Region: PRK15455 998088006393 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 998088006394 Walker A motif; other site 998088006395 ATP binding site [chemical binding]; other site 998088006396 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 998088006397 hypothetical protein; Provisional; Region: PRK05325 998088006398 SpoVR family protein; Provisional; Region: PRK11767 998088006399 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 998088006400 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 998088006401 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 998088006402 substrate binding site [chemical binding]; other site 998088006403 oxyanion hole (OAH) forming residues; other site 998088006404 trimer interface [polypeptide binding]; other site 998088006405 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 998088006406 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 998088006407 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 998088006408 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 998088006409 dimer interface [polypeptide binding]; other site 998088006410 active site 998088006411 MoxR-like ATPases [General function prediction only]; Region: COG0714 998088006412 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 998088006413 Walker A motif; other site 998088006414 ATP binding site [chemical binding]; other site 998088006415 Walker B motif; other site 998088006416 arginine finger; other site 998088006417 Protein of unknown function DUF58; Region: DUF58; pfam01882 998088006418 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 998088006419 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 998088006420 metal ion-dependent adhesion site (MIDAS); other site 998088006421 von Willebrand factor type A domain; Region: VWA_2; pfam13519 998088006422 metal ion-dependent adhesion site (MIDAS); other site 998088006423 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 998088006424 TPR repeat; Region: TPR_11; pfam13414 998088006425 TPR motif; other site 998088006426 binding surface 998088006427 Oxygen tolerance; Region: BatD; pfam13584 998088006428 RNA polymerase sigma factor; Provisional; Region: PRK12517 998088006429 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088006430 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 998088006431 DNA binding residues [nucleotide binding] 998088006432 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 998088006433 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 998088006434 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 998088006435 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 998088006436 EAL domain; Region: EAL; pfam00563 998088006437 putative acyltransferase; Provisional; Region: PRK05790 998088006438 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 998088006439 dimer interface [polypeptide binding]; other site 998088006440 active site 998088006441 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 998088006442 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 998088006443 DNA binding residues [nucleotide binding] 998088006444 putative dimer interface [polypeptide binding]; other site 998088006445 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 998088006446 CTC domain interface [polypeptide binding]; other site 998088006447 L16 interface [polypeptide binding]; other site 998088006448 ATP-dependent RNA helicase HrpA; Provisional; Region: PRK11131 998088006449 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 998088006450 ATP binding site [chemical binding]; other site 998088006451 putative Mg++ binding site [ion binding]; other site 998088006452 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 998088006453 nucleotide binding region [chemical binding]; other site 998088006454 ATP-binding site [chemical binding]; other site 998088006455 Helicase associated domain (HA2); Region: HA2; pfam04408 998088006456 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 998088006457 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 998088006458 FOG: CBS domain [General function prediction only]; Region: COG0517 998088006459 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_16; cd04629 998088006460 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088006461 Zn2+ binding site [ion binding]; other site 998088006462 Mg2+ binding site [ion binding]; other site 998088006463 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 998088006464 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088006465 Zn2+ binding site [ion binding]; other site 998088006466 Mg2+ binding site [ion binding]; other site 998088006467 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 998088006468 Sulfatase; Region: Sulfatase; pfam00884 998088006469 MoxR-like ATPases [General function prediction only]; Region: COG0714 998088006470 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 998088006471 Walker A motif; other site 998088006472 ATP binding site [chemical binding]; other site 998088006473 Walker B motif; other site 998088006474 arginine finger; other site 998088006475 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 998088006476 Protein of unknown function DUF58; Region: DUF58; pfam01882 998088006477 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 998088006478 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 998088006479 metal ion-dependent adhesion site (MIDAS); other site 998088006480 von Willebrand factor type A domain; Region: VWA_2; pfam13519 998088006481 metal ion-dependent adhesion site (MIDAS); other site 998088006482 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 998088006483 binding surface 998088006484 TPR motif; other site 998088006485 Oxygen tolerance; Region: BatD; pfam13584 998088006486 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 998088006487 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088006488 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 998088006489 dimerization interface [polypeptide binding]; other site 998088006490 Uncharacterized conserved protein [Function unknown]; Region: COG1262 998088006491 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 998088006492 HEAT repeats; Region: HEAT_2; pfam13646 998088006493 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 998088006494 TPR motif; other site 998088006495 TPR repeat; Region: TPR_11; pfam13414 998088006496 binding surface 998088006497 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 998088006498 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 998088006499 FeS/SAM binding site; other site 998088006500 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 998088006501 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088006502 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006503 metal binding site [ion binding]; metal-binding site 998088006504 active site 998088006505 I-site; other site 998088006506 uncharacterized phage protein; Region: phage_xxxx; TIGR02642 998088006507 Protein of unknown function (DUF1364); Region: DUF1364; pfam07102 998088006508 Protein of unknown function (DUF1367); Region: DUF1367; pfam07105 998088006509 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088006510 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 998088006511 dimerization interface [polypeptide binding]; other site 998088006512 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088006513 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088006514 dimer interface [polypeptide binding]; other site 998088006515 putative CheW interface [polypeptide binding]; other site 998088006516 nitrobindin heme-binding domain; Region: nitrobindin; cl10502 998088006517 heme-binding site [chemical binding]; other site 998088006518 N-glycosyltransferase; Provisional; Region: PRK11204 998088006519 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 998088006520 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 998088006521 DXD motif; other site 998088006522 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088006523 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088006524 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 998088006525 lipoyl-biotinyl attachment site [posttranslational modification]; other site 998088006526 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 998088006527 Transposase; Region: DEDD_Tnp_IS110; pfam01548 998088006528 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 998088006529 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 998088006530 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 998088006531 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 998088006532 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 998088006533 active site 998088006534 Int/Topo IB signature motif; other site 998088006535 DNA binding site [nucleotide binding] 998088006536 exonuclease I; Provisional; Region: sbcB; PRK11779 998088006537 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 998088006538 active site 998088006539 catalytic site [active] 998088006540 substrate binding site [chemical binding]; other site 998088006541 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 998088006542 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 998088006543 Melibiase; Region: Melibiase; pfam02065 998088006544 LrgA family; Region: LrgA; cl00608 998088006545 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 998088006546 cytidine deaminase; Provisional; Region: PRK09027 998088006547 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 998088006548 active site 998088006549 catalytic motif [active] 998088006550 Zn binding site [ion binding]; other site 998088006551 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 998088006552 active site 998088006553 catalytic motif [active] 998088006554 Zn binding site [ion binding]; other site 998088006555 tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional; Region: tnaA; PRK13238 998088006556 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 998088006557 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088006558 catalytic residue [active] 998088006559 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; pfam10013 998088006560 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 998088006561 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 998088006562 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 998088006563 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 998088006564 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 998088006565 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 998088006566 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]; Region: FhlA; COG3604 998088006567 GAF domain; Region: GAF; pfam01590 998088006568 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 998088006569 Walker A motif; other site 998088006570 ATP binding site [chemical binding]; other site 998088006571 Walker B motif; other site 998088006572 arginine finger; other site 998088006573 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 998088006574 formate dehydrogenase-H ferredoxin subunit; Provisional; Region: PRK10330 998088006575 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 998088006576 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088006577 Coenzyme A binding pocket [chemical binding]; other site 998088006578 potassium transport protein Kup; Provisional; Region: trkD; PRK10745 998088006579 potassium uptake protein; Region: kup; TIGR00794 998088006580 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cl00179 998088006581 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 998088006582 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 998088006583 active site 998088006584 intersubunit interface [polypeptide binding]; other site 998088006585 catalytic residue [active] 998088006586 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 998088006587 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 998088006588 substrate binding site [chemical binding]; other site 998088006589 ATP binding site [chemical binding]; other site 998088006590 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 998088006591 2-deoxy-D-gluconate 3-dehydrogenase; Validated; Region: PRK08993 998088006592 gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs; Region: Ga5DH-like_SDR_c; cd05347 998088006593 NADP binding site [chemical binding]; other site 998088006594 homodimer interface [polypeptide binding]; other site 998088006595 active site 998088006596 5-keto-4-deoxyuronate isomerase; Provisional; Region: PRK00924 998088006597 putative outer membrane porin protein; Provisional; Region: PRK11379 998088006598 outer membrane porin, OprD family; Region: OprD; pfam03573 998088006599 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 998088006600 Glycosyl Hydrolase Family 88; Region: Glyco_hydro_88; pfam07470 998088006601 hypothetical protein; Provisional; Region: PRK02947 998088006602 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 998088006603 putative active site [active] 998088006604 PTS system sorbose subfamily IIB component; Region: PTSIIB_sorb; pfam03830 998088006605 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; pfam03613 998088006606 PTS system sorbose-specific iic component; Region: EII-Sor; pfam03609 998088006607 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 998088006608 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088006609 DNA-binding site [nucleotide binding]; DNA binding site 998088006610 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 998088006611 4Fe-4S dicluster domain; Region: Fer4_11; pfam13247 998088006612 4Fe-4S binding domain; Region: Fer4; pfam00037 998088006613 hydrogenase 4 subunit B; Validated; Region: PRK06521 998088006614 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 998088006615 NADH dehydrogenase; Region: NADHdh; cl00469 998088006616 Ni,Fe-hydrogenase III component G [Energy production and conversion]; Region: HycE; COG3262 998088006617 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 998088006618 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 998088006619 hydrogenase 4 subunit H; Validated; Region: PRK08222 998088006620 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 998088006621 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]; Region: COG3260 998088006622 Formate hydrogenlyase maturation protein HycH; Region: HycH; pfam07450 998088006623 Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation...; Region: H2MP_MemB-H2evol; cd06067 998088006624 nickel binding site [ion binding]; other site 998088006625 seryl-tRNA(sec) selenium transferase; Region: selA; TIGR00474 998088006626 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 998088006627 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 998088006628 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088006629 catalytic residue [active] 998088006630 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 998088006631 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 998088006632 G1 box; other site 998088006633 GTP/Mg2+ binding site [chemical binding]; other site 998088006634 G2 box; other site 998088006635 Switch I region; other site 998088006636 G3 box; other site 998088006637 Switch II region; other site 998088006638 G4 box; other site 998088006639 G5 box; other site 998088006640 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 998088006641 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 998088006642 Acylphosphatase; Region: Acylphosphatase; pfam00708 998088006643 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 998088006644 HypF finger; Region: zf-HYPF; pfam07503 998088006645 HypF finger; Region: zf-HYPF; pfam07503 998088006646 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 998088006647 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 998088006648 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 998088006649 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 998088006650 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 998088006651 dimerization interface [polypeptide binding]; other site 998088006652 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 998088006653 ATP binding site [chemical binding]; other site 998088006654 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 998088006655 Hydrogenase expression/synthesis hypA family; Region: HypA; cl17671 998088006656 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 998088006657 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 998088006658 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 998088006659 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088006660 Walker A/P-loop; other site 998088006661 ATP binding site [chemical binding]; other site 998088006662 Q-loop/lid; other site 998088006663 ABC transporter signature motif; other site 998088006664 Walker B; other site 998088006665 D-loop; other site 998088006666 H-loop/switch region; other site 998088006667 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088006668 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 998088006669 Walker A/P-loop; other site 998088006670 ATP binding site [chemical binding]; other site 998088006671 Q-loop/lid; other site 998088006672 ABC transporter signature motif; other site 998088006673 Walker B; other site 998088006674 D-loop; other site 998088006675 H-loop/switch region; other site 998088006676 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 998088006677 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 998088006678 dimer interface [polypeptide binding]; other site 998088006679 conserved gate region; other site 998088006680 ABC-ATPase subunit interface; other site 998088006681 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 998088006682 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 998088006683 dimer interface [polypeptide binding]; other site 998088006684 conserved gate region; other site 998088006685 putative PBP binding loops; other site 998088006686 ABC-ATPase subunit interface; other site 998088006687 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_19; cd08518 998088006688 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 998088006689 hydrogenase 2-specific chaperone; Provisional; Region: PRK10465 998088006690 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 998088006691 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 998088006692 putative substrate-binding site; other site 998088006693 nickel binding site [ion binding]; other site 998088006694 hydrogenase 2 large subunit; Provisional; Region: PRK10467 998088006695 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 998088006696 putative hydrogenase 2 b cytochrome subunit; Provisional; Region: PRK10881 998088006697 hydrogenase 2 protein HybA; Provisional; Region: PRK10882 998088006698 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 998088006699 4Fe-4S binding domain; Region: Fer4; cl02805 998088006700 hydrogenase 2 small subunit; Provisional; Region: PRK10468 998088006701 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 998088006702 SnoaL-like domain; Region: SnoaL_3; pfam13474 998088006703 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088006704 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088006705 metal binding site [ion binding]; metal-binding site 998088006706 active site 998088006707 I-site; other site 998088006708 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088006709 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 998088006710 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 998088006711 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088006712 O-Antigen ligase; Region: Wzy_C; cl04850 998088006713 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 998088006714 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 998088006715 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 998088006716 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 998088006717 trimer interface [polypeptide binding]; other site 998088006718 active site 998088006719 substrate binding site [chemical binding]; other site 998088006720 CoA binding site [chemical binding]; other site 998088006721 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: GT1_like_1; cd04950 998088006722 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088006723 putative homodimer interface [polypeptide binding]; other site 998088006724 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; cd00198 998088006725 metal ion-dependent adhesion site (MIDAS); other site 998088006726 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 998088006727 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 998088006728 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 998088006729 CESA_like_1 is a member of the cellulose synthase (CESA) superfamily; Region: CESA_like_1; cd06439 998088006730 DXD motif; other site 998088006731 Bacterial sugar transferase; Region: Bac_transf; pfam02397 998088006732 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088006733 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 998088006734 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 998088006735 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 998088006736 ATP binding site [chemical binding]; other site 998088006737 Mg2+ binding site [ion binding]; other site 998088006738 G-X-G motif; other site 998088006739 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088006740 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 998088006741 active site 998088006742 phosphorylation site [posttranslational modification] 998088006743 intermolecular recognition site; other site 998088006744 dimerization interface [polypeptide binding]; other site 998088006745 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 998088006746 AAA domain; Region: AAA_31; pfam13614 998088006747 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 998088006748 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 998088006749 SLBB domain; Region: SLBB; pfam10531 998088006750 SLBB domain; Region: SLBB; pfam10531 998088006751 SLBB domain; Region: SLBB; pfam10531 998088006752 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 998088006753 SLBB domain; Region: SLBB; pfam10531 998088006754 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 998088006755 anti sigma factor interaction site; other site 998088006756 regulatory phosphorylation site [posttranslational modification]; other site 998088006757 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 998088006758 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088006759 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 998088006760 dimer interface [polypeptide binding]; other site 998088006761 phosphorylation site [posttranslational modification] 998088006762 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 998088006763 ATP binding site [chemical binding]; other site 998088006764 Mg2+ binding site [ion binding]; other site 998088006765 G-X-G motif; other site 998088006766 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088006767 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 998088006768 active site 998088006769 phosphorylation site [posttranslational modification] 998088006770 intermolecular recognition site; other site 998088006771 dimerization interface [polypeptide binding]; other site 998088006772 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088006773 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088006774 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_5; cd08474 998088006775 putative effector binding pocket; other site 998088006776 putative dimerization interface [polypeptide binding]; other site 998088006777 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 998088006778 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 998088006779 Uncharacterized conserved protein [Function unknown]; Region: COG4925 998088006780 ribonucleoside transporter; Reviewed; Region: nepI; PRK10213 998088006781 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 998088006782 putative substrate translocation pore; other site 998088006783 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 998088006784 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 998088006785 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 998088006786 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088006787 NAD(P) binding site [chemical binding]; other site 998088006788 active site 998088006789 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 998088006790 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 998088006791 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 998088006792 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 998088006793 substrate binding site [chemical binding]; other site 998088006794 oxyanion hole (OAH) forming residues; other site 998088006795 trimer interface [polypeptide binding]; other site 998088006796 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 998088006797 enoyl-CoA hydratase; Provisional; Region: PRK09076 998088006798 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 998088006799 substrate binding site [chemical binding]; other site 998088006800 oxyanion hole (OAH) forming residues; other site 998088006801 trimer interface [polypeptide binding]; other site 998088006802 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 998088006803 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 998088006804 active site 998088006805 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 998088006806 isovaleryl-CoA dehydrogenase; Region: PLN02519 998088006807 substrate binding site [chemical binding]; other site 998088006808 FAD binding site [chemical binding]; other site 998088006809 catalytic base [active] 998088006810 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 998088006811 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 998088006812 enoyl-CoA hydratase; Provisional; Region: PRK05995 998088006813 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 998088006814 substrate binding site [chemical binding]; other site 998088006815 oxyanion hole (OAH) forming residues; other site 998088006816 trimer interface [polypeptide binding]; other site 998088006817 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 998088006818 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 998088006819 ATP-grasp domain; Region: ATP-grasp_4; cl17255 998088006820 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 998088006821 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 998088006822 carboxyltransferase (CT) interaction site; other site 998088006823 biotinylation site [posttranslational modification]; other site 998088006824 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 998088006825 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 998088006826 active site 998088006827 catalytic residues [active] 998088006828 metal binding site [ion binding]; metal-binding site 998088006829 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 998088006830 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 998088006831 DNA binding residues [nucleotide binding] 998088006832 putative dimer interface [polypeptide binding]; other site 998088006833 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 998088006834 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 998088006835 substrate binding pocket [chemical binding]; other site 998088006836 membrane-bound complex binding site; other site 998088006837 hinge residues; other site 998088006838 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 998088006839 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 998088006840 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 998088006841 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 998088006842 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 998088006843 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 998088006844 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 998088006845 amino acid carrier protein; Region: agcS; TIGR00835 998088006846 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 998088006847 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 998088006848 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 998088006849 Transposase; Region: DEDD_Tnp_IS110; pfam01548 998088006850 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 998088006851 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 998088006852 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 998088006853 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 998088006854 Phage-related protein [Function unknown]; Region: COG4695; cl01923 998088006855 Integrase core domain; Region: rve_3; pfam13683 998088006856 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 998088006857 IS2 transposase TnpB; Reviewed; Region: PRK09409 998088006858 HTH-like domain; Region: HTH_21; pfam13276 998088006859 Integrase core domain; Region: rve; pfam00665 998088006860 Integrase core domain; Region: rve_3; pfam13683 998088006861 Transposase; Region: HTH_Tnp_1; cl17663 998088006862 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 998088006863 Phage-related protein [Function unknown]; Region: COG4695; cl01923 998088006864 enoyl-CoA hydratase; Provisional; Region: PRK07509 998088006865 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 998088006866 substrate binding site [chemical binding]; other site 998088006867 oxyanion hole (OAH) forming residues; other site 998088006868 trimer interface [polypeptide binding]; other site 998088006869 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 998088006870 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 998088006871 ligand binding site [chemical binding]; other site 998088006872 flexible hinge region; other site 998088006873 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 998088006874 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 998088006875 metal binding triad; other site 998088006876 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 998088006877 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 998088006878 active site 998088006879 catalytic site [active] 998088006880 substrate binding site [chemical binding]; other site 998088006881 Predicted membrane protein [Function unknown]; Region: COG3162 998088006882 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 998088006883 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 998088006884 Na binding site [ion binding]; other site 998088006885 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 998088006886 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088006887 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088006888 ABC transporter; Region: ABC_tran_2; pfam12848 998088006889 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088006890 periplasmic folding chaperone; Provisional; Region: PRK10788 998088006891 SurA N-terminal domain; Region: SurA_N_3; cl07813 998088006892 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 998088006893 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 998088006894 IHF dimer interface [polypeptide binding]; other site 998088006895 IHF - DNA interface [nucleotide binding]; other site 998088006896 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 998088006897 Found in ATP-dependent protease La (LON); Region: LON; smart00464 998088006898 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 998088006899 Walker A motif; other site 998088006900 ATP binding site [chemical binding]; other site 998088006901 Walker B motif; other site 998088006902 arginine finger; other site 998088006903 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 998088006904 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 998088006905 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 998088006906 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 998088006907 Walker A motif; other site 998088006908 ATP binding site [chemical binding]; other site 998088006909 Walker B motif; other site 998088006910 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 998088006911 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 998088006912 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 998088006913 oligomer interface [polypeptide binding]; other site 998088006914 active site residues [active] 998088006915 trigger factor; Provisional; Region: tig; PRK01490 998088006916 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 998088006917 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 998088006918 hypothetical protein; Provisional; Region: PRK11770 998088006919 Domain of unknown function (DUF307); Region: DUF307; pfam03733 998088006920 Domain of unknown function (DUF307); Region: DUF307; pfam03733 998088006921 5'-nucleotidase; Provisional; Region: PRK03826 998088006922 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 998088006923 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088006924 FtsX-like permease family; Region: FtsX; pfam02687 998088006925 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 998088006926 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 998088006927 Walker A/P-loop; other site 998088006928 ATP binding site [chemical binding]; other site 998088006929 Q-loop/lid; other site 998088006930 ABC transporter signature motif; other site 998088006931 Walker B; other site 998088006932 D-loop; other site 998088006933 H-loop/switch region; other site 998088006934 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 998088006935 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088006936 FtsX-like permease family; Region: FtsX; pfam02687 998088006937 transcription-repair coupling factor; Provisional; Region: PRK10689 998088006938 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 998088006939 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 998088006940 ATP binding site [chemical binding]; other site 998088006941 putative Mg++ binding site [ion binding]; other site 998088006942 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 998088006943 nucleotide binding region [chemical binding]; other site 998088006944 ATP-binding site [chemical binding]; other site 998088006945 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 998088006946 fructose-1,6-bisphosphatase family protein; Region: PLN02628 998088006947 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 998088006948 AMP binding site [chemical binding]; other site 998088006949 metal binding site [ion binding]; metal-binding site 998088006950 active site 998088006951 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 998088006952 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 998088006953 peptide binding site [polypeptide binding]; other site 998088006954 EamA-like transporter family; Region: EamA; pfam00892 998088006955 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 998088006956 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 998088006957 catalytic core [active] 998088006958 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 998088006959 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 998088006960 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 998088006961 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 998088006962 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 998088006963 Leucine rich repeat; Region: LRR_8; pfam13855 998088006964 Leucine rich repeat; Region: LRR_8; pfam13855 998088006965 Protein tyrosine kinase; Region: Pkinase_Tyr; pfam07714 998088006966 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 998088006967 active site 998088006968 ATP binding site [chemical binding]; other site 998088006969 substrate binding site [chemical binding]; other site 998088006970 activation loop (A-loop); other site 998088006971 GMP synthase; Reviewed; Region: guaA; PRK00074 998088006972 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 998088006973 AMP/PPi binding site [chemical binding]; other site 998088006974 candidate oxyanion hole; other site 998088006975 catalytic triad [active] 998088006976 potential glutamine specificity residues [chemical binding]; other site 998088006977 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 998088006978 ATP Binding subdomain [chemical binding]; other site 998088006979 Ligand Binding sites [chemical binding]; other site 998088006980 Dimerization subdomain; other site 998088006981 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 998088006982 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 998088006983 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 998088006984 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 998088006985 active site 998088006986 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 998088006987 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 998088006988 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 998088006989 generic binding surface II; other site 998088006990 generic binding surface I; other site 998088006991 DNA-binding transcriptional repressor MngR; Provisional; Region: PRK09764 998088006992 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088006993 DNA-binding site [nucleotide binding]; DNA binding site 998088006994 UTRA domain; Region: UTRA; pfam07702 998088006995 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 998088006996 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 998088006997 active site 998088006998 phosphorylation site [posttranslational modification] 998088006999 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 998088007000 active site 998088007001 P-loop; other site 998088007002 phosphorylation site [posttranslational modification] 998088007003 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; COG1299 998088007004 alpha-mannosidase; Provisional; Region: PRK09819 998088007005 N-terminal catalytic domain of Escherichia coli alpha-mannosidase MngB and its bacterial homologs; glycoside hydrolase family 38 (GH38); Region: GH38N_AMII_EcMngB_like; cd10815 998088007006 active site 998088007007 metal binding site [ion binding]; metal-binding site 998088007008 catalytic site [active] 998088007009 Alpha mannosidase, middle domain; Region: Alpha-mann_mid; smart00872 998088007010 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 998088007011 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 998088007012 ATP-grasp domain; Region: ATP-grasp_4; cl17255 998088007013 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 998088007014 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 998088007015 catalytic residues [active] 998088007016 dimer interface [polypeptide binding]; other site 998088007017 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; cl17251 998088007018 ATP binding site [chemical binding]; other site 998088007019 putative Mg++ binding site [ion binding]; other site 998088007020 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 998088007021 nucleotide binding region [chemical binding]; other site 998088007022 ATP-binding site [chemical binding]; other site 998088007023 coproporphyrinogen III oxidase; Provisional; Region: PRK09058 998088007024 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 998088007025 FeS/SAM binding site; other site 998088007026 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 998088007027 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 998088007028 dimerization interface [polypeptide binding]; other site 998088007029 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088007030 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088007031 dimer interface [polypeptide binding]; other site 998088007032 putative CheW interface [polypeptide binding]; other site 998088007033 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 998088007034 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088007035 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 998088007036 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 998088007037 hinge; other site 998088007038 active site 998088007039 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 998088007040 homodimer interface [polypeptide binding]; other site 998088007041 substrate-cofactor binding pocket; other site 998088007042 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088007043 catalytic residue [active] 998088007044 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 998088007045 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 998088007046 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 998088007047 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 998088007048 Ligand binding site [chemical binding]; other site 998088007049 Electron transfer flavoprotein domain; Region: ETF; pfam01012 998088007050 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 998088007051 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 998088007052 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 998088007053 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 998088007054 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 998088007055 Cl binding site [ion binding]; other site 998088007056 oligomer interface [polypeptide binding]; other site 998088007057 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 998088007058 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 998088007059 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 998088007060 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 998088007061 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 998088007062 ligand binding site; other site 998088007063 oligomer interface; other site 998088007064 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 998088007065 dimer interface [polypeptide binding]; other site 998088007066 N-terminal domain interface [polypeptide binding]; other site 998088007067 sulfate 1 binding site; other site 998088007068 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088007069 metal binding site [ion binding]; metal-binding site 998088007070 active site 998088007071 I-site; other site 998088007072 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 998088007073 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 998088007074 inosine/guanosine kinase; Provisional; Region: PRK15074 998088007075 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 998088007076 substrate binding site [chemical binding]; other site 998088007077 ATP binding site [chemical binding]; other site 998088007078 MAPEG family; Region: MAPEG; cl09190 998088007079 ferrochelatase; Reviewed; Region: hemH; PRK00035 998088007080 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 998088007081 C-terminal domain interface [polypeptide binding]; other site 998088007082 active site 998088007083 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 998088007084 active site 998088007085 N-terminal domain interface [polypeptide binding]; other site 998088007086 adenylate kinase; Reviewed; Region: adk; PRK00279 998088007087 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 998088007088 AMP-binding site [chemical binding]; other site 998088007089 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 998088007090 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 998088007091 active site 998088007092 dinuclear metal binding site [ion binding]; other site 998088007093 dimerization interface [polypeptide binding]; other site 998088007094 amidophosphoribosyltransferase; Provisional; Region: PRK09246 998088007095 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 998088007096 active site 998088007097 tetramer interface [polypeptide binding]; other site 998088007098 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 998088007099 active site 998088007100 Colicin V production protein; Region: Colicin_V; cl00567 998088007101 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 998088007102 seryl-tRNA synthetase; Provisional; Region: PRK05431 998088007103 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 998088007104 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 998088007105 dimer interface [polypeptide binding]; other site 998088007106 active site 998088007107 motif 1; other site 998088007108 motif 2; other site 998088007109 motif 3; other site 998088007110 recombination factor protein RarA; Reviewed; Region: PRK13342 998088007111 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 998088007112 Walker A motif; other site 998088007113 ATP binding site [chemical binding]; other site 998088007114 Walker B motif; other site 998088007115 arginine finger; other site 998088007116 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 998088007117 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 998088007118 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 998088007119 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 998088007120 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 998088007121 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 998088007122 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 998088007123 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 998088007124 putative DNA binding site [nucleotide binding]; other site 998088007125 putative Zn2+ binding site [ion binding]; other site 998088007126 AsnC family; Region: AsnC_trans_reg; pfam01037 998088007127 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 998088007128 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 998088007129 hexamer interface [polypeptide binding]; other site 998088007130 ligand binding site [chemical binding]; other site 998088007131 putative active site [active] 998088007132 NAD(P) binding site [chemical binding]; other site 998088007133 thioredoxin reductase; Provisional; Region: PRK10262 998088007134 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088007135 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088007136 Response regulator receiver domain; Region: Response_reg; pfam00072 998088007137 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 998088007138 active site 998088007139 phosphorylation site [posttranslational modification] 998088007140 intermolecular recognition site; other site 998088007141 dimerization interface [polypeptide binding]; other site 998088007142 Response regulator receiver domain; Region: Response_reg; pfam00072 998088007143 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 998088007144 active site 998088007145 phosphorylation site [posttranslational modification] 998088007146 intermolecular recognition site; other site 998088007147 dimerization interface [polypeptide binding]; other site 998088007148 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088007149 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088007150 metal binding site [ion binding]; metal-binding site 998088007151 active site 998088007152 I-site; other site 998088007153 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 998088007154 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 998088007155 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 998088007156 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 998088007157 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 998088007158 rRNA binding site [nucleotide binding]; other site 998088007159 predicted 30S ribosome binding site; other site 998088007160 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 998088007161 Clp amino terminal domain; Region: Clp_N; pfam02861 998088007162 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 998088007163 Walker A motif; other site 998088007164 ATP binding site [chemical binding]; other site 998088007165 Walker B motif; other site 998088007166 arginine finger; other site 998088007167 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 998088007168 Walker A motif; other site 998088007169 ATP binding site [chemical binding]; other site 998088007170 Walker B motif; other site 998088007171 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 998088007172 Uncharacterized conserved protein [Function unknown]; Region: COG2127 998088007173 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 998088007174 DNA-binding site [nucleotide binding]; DNA binding site 998088007175 RNA-binding motif; other site 998088007176 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 998088007177 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 998088007178 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 998088007179 homodimer interface [polypeptide binding]; other site 998088007180 NADP binding site [chemical binding]; other site 998088007181 substrate binding site [chemical binding]; other site 998088007182 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 998088007183 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 998088007184 active site 998088007185 phosphorylation site [posttranslational modification] 998088007186 intermolecular recognition site; other site 998088007187 dimerization interface [polypeptide binding]; other site 998088007188 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 998088007189 DNA binding site [nucleotide binding] 998088007190 sensor protein RstB; Provisional; Region: PRK10604 998088007191 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 998088007192 dimerization interface [polypeptide binding]; other site 998088007193 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 998088007194 dimer interface [polypeptide binding]; other site 998088007195 phosphorylation site [posttranslational modification] 998088007196 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 998088007197 ATP binding site [chemical binding]; other site 998088007198 Mg2+ binding site [ion binding]; other site 998088007199 G-X-G motif; other site 998088007200 Predicted integral membrane protein [Function unknown]; Region: COG0392 998088007201 Uncharacterized conserved protein [Function unknown]; Region: COG2898 998088007202 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 998088007203 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 998088007204 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 998088007205 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 998088007206 Domain of unknown function (DUF1704); Region: DUF1704; pfam08014 998088007207 thymidine kinase; Provisional; Region: PRK04296 998088007208 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 998088007209 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 998088007210 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 998088007211 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 998088007212 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 998088007213 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 998088007214 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 998088007215 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 998088007216 Ligand Binding Site [chemical binding]; other site 998088007217 DTW domain; Region: DTW; pfam03942 998088007218 rhomboid family GlyGly-CTERM serine protease; Region: rhom_GG_sort; TIGR03902 998088007219 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 998088007220 active site 998088007221 dimer interface [polypeptide binding]; other site 998088007222 tetratricopeptide repeat protein; Provisional; Region: PRK11788 998088007223 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 998088007224 TPR motif; other site 998088007225 binding surface 998088007226 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 998088007227 binding surface 998088007228 TPR motif; other site 998088007229 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 998088007230 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 998088007231 IHF dimer interface [polypeptide binding]; other site 998088007232 IHF - DNA interface [nucleotide binding]; other site 998088007233 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 998088007234 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 998088007235 RNA binding site [nucleotide binding]; other site 998088007236 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 998088007237 RNA binding site [nucleotide binding]; other site 998088007238 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 998088007239 RNA binding site [nucleotide binding]; other site 998088007240 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 998088007241 RNA binding site [nucleotide binding]; other site 998088007242 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 998088007243 RNA binding site [nucleotide binding]; other site 998088007244 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 998088007245 RNA binding site [nucleotide binding]; other site 998088007246 cytidylate kinase; Provisional; Region: cmk; PRK00023 998088007247 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 998088007248 CMP-binding site; other site 998088007249 The sites determining sugar specificity; other site 998088007250 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 998088007251 dimerization interface [polypeptide binding]; other site 998088007252 active site 998088007253 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 998088007254 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088007255 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 998088007256 dimerization interface [polypeptide binding]; other site 998088007257 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 998088007258 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088007259 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 998088007260 dimerization interface [polypeptide binding]; other site 998088007261 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 998088007262 Major Facilitator Superfamily; Region: MFS_1; pfam07690 998088007263 putative substrate translocation pore; other site 998088007264 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 998088007265 active site 998088007266 metal binding site [ion binding]; metal-binding site 998088007267 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as...; Region: NfsA_FRP; cd02146 998088007268 dimer interface [polypeptide binding]; other site 998088007269 FMN binding site [chemical binding]; other site 998088007270 NADPH bind site [chemical binding]; other site 998088007271 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 998088007272 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 998088007273 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088007274 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088007275 metal binding site [ion binding]; metal-binding site 998088007276 active site 998088007277 I-site; other site 998088007278 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 998088007279 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088007280 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088007281 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 998088007282 putative effector binding pocket; other site 998088007283 dimerization interface [polypeptide binding]; other site 998088007284 Response regulator receiver domain; Region: Response_reg; pfam00072 998088007285 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 998088007286 active site 998088007287 phosphorylation site [posttranslational modification] 998088007288 intermolecular recognition site; other site 998088007289 dimerization interface [polypeptide binding]; other site 998088007290 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 998088007291 PAS domain; Region: PAS; smart00091 998088007292 PAS fold; Region: PAS_4; pfam08448 998088007293 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 998088007294 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 998088007295 tetramer interface [polypeptide binding]; other site 998088007296 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088007297 catalytic residue [active] 998088007298 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088007299 NAD(P) binding site [chemical binding]; other site 998088007300 active site 998088007301 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 998088007302 non-specific DNA binding site [nucleotide binding]; other site 998088007303 salt bridge; other site 998088007304 sequence-specific DNA binding site [nucleotide binding]; other site 998088007305 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 998088007306 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 998088007307 active site 998088007308 catalytic tetrad [active] 998088007309 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 998088007310 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 998088007311 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 998088007312 Walker A/P-loop; other site 998088007313 ATP binding site [chemical binding]; other site 998088007314 Q-loop/lid; other site 998088007315 ABC transporter signature motif; other site 998088007316 Walker B; other site 998088007317 D-loop; other site 998088007318 H-loop/switch region; other site 998088007319 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 998088007320 dimer interface [polypeptide binding]; other site 998088007321 conserved gate region; other site 998088007322 putative PBP binding loops; other site 998088007323 ABC-ATPase subunit interface; other site 998088007324 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 998088007325 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007326 substrate binding pocket [chemical binding]; other site 998088007327 membrane-bound complex binding site; other site 998088007328 hinge residues; other site 998088007329 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088007330 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 998088007331 dimer interface [polypeptide binding]; other site 998088007332 conserved gate region; other site 998088007333 putative PBP binding loops; other site 998088007334 ABC-ATPase subunit interface; other site 998088007335 penicillin-insensitive murein endopeptidase; Reviewed; Region: mepA; PRK09429 998088007336 LemA family; Region: LemA; pfam04011 998088007337 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 998088007338 Repair protein; Region: Repair_PSII; pfam04536 998088007339 Repair protein; Region: Repair_PSII; cl01535 998088007340 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088007341 flagellar motor protein MotP; Reviewed; Region: PRK06743 998088007342 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 998088007343 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 998088007344 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088007345 ligand binding site [chemical binding]; other site 998088007346 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 998088007347 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 998088007348 N-terminal plug; other site 998088007349 ligand-binding site [chemical binding]; other site 998088007350 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 998088007351 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 998088007352 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 998088007353 Zn binding site [ion binding]; other site 998088007354 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 998088007355 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 998088007356 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 998088007357 NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]; Region: NuoB; COG0377 998088007358 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 998088007359 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 998088007360 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 998088007361 NADH dehydrogenase subunit E; Validated; Region: PRK07539 998088007362 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 998088007363 putative dimer interface [polypeptide binding]; other site 998088007364 [2Fe-2S] cluster binding site [ion binding]; other site 998088007365 NADH dehydrogenase I subunit F; Provisional; Region: PRK11278 998088007366 SLBB domain; Region: SLBB; pfam10531 998088007367 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 998088007368 NADH-quinone oxidoreductase, chain G; Region: NuoG; TIGR01973 998088007369 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 998088007370 catalytic loop [active] 998088007371 iron binding site [ion binding]; other site 998088007372 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; smart00929 998088007373 MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory...; Region: MopB_NDH-1_NuoG2-N7; cd02771 998088007374 [4Fe-4S] binding site [ion binding]; other site 998088007375 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex...; Region: MopB_CT_NDH-1_NuoG2-N7; cd02788 998088007376 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 998088007377 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 998088007378 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 998088007379 4Fe-4S binding domain; Region: Fer4; pfam00037 998088007380 4Fe-4S binding domain; Region: Fer4; pfam00037 998088007381 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 998088007382 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 998088007383 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 998088007384 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 998088007385 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 998088007386 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 998088007387 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 998088007388 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 998088007389 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 998088007390 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 998088007391 FIST N domain; Region: FIST; cl10701 998088007392 FIST C domain; Region: FIST_C; pfam10442 998088007393 PAS fold; Region: PAS_4; pfam08448 998088007394 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 998088007395 putative active site [active] 998088007396 heme pocket [chemical binding]; other site 998088007397 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 998088007398 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088007399 Zn2+ binding site [ion binding]; other site 998088007400 Mg2+ binding site [ion binding]; other site 998088007401 PAS fold; Region: PAS_4; pfam08448 998088007402 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 998088007403 putative active site [active] 998088007404 heme pocket [chemical binding]; other site 998088007405 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 998088007406 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088007407 Zn2+ binding site [ion binding]; other site 998088007408 Mg2+ binding site [ion binding]; other site 998088007409 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 998088007410 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 998088007411 dimerization interface [polypeptide binding]; other site 998088007412 ATP binding site [chemical binding]; other site 998088007413 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 998088007414 dimerization interface [polypeptide binding]; other site 998088007415 ATP binding site [chemical binding]; other site 998088007416 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 998088007417 putative active site [active] 998088007418 catalytic triad [active] 998088007419 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 998088007420 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 998088007421 substrate binding pocket [chemical binding]; other site 998088007422 membrane-bound complex binding site; other site 998088007423 hinge residues; other site 998088007424 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 998088007425 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088007426 catalytic residue [active] 998088007427 Protein of unknown function (DUF1407); Region: DUF1407; pfam07191 998088007428 GTP-binding protein Der; Reviewed; Region: PRK00093 998088007429 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 998088007430 G1 box; other site 998088007431 GTP/Mg2+ binding site [chemical binding]; other site 998088007432 Switch I region; other site 998088007433 G2 box; other site 998088007434 Switch II region; other site 998088007435 G3 box; other site 998088007436 G4 box; other site 998088007437 G5 box; other site 998088007438 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 998088007439 G1 box; other site 998088007440 GTP/Mg2+ binding site [chemical binding]; other site 998088007441 Switch I region; other site 998088007442 G2 box; other site 998088007443 G3 box; other site 998088007444 Switch II region; other site 998088007445 G4 box; other site 998088007446 G5 box; other site 998088007447 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 998088007448 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 998088007449 Trp docking motif [polypeptide binding]; other site 998088007450 active site 998088007451 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 998088007452 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 998088007453 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 998088007454 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 998088007455 dimer interface [polypeptide binding]; other site 998088007456 motif 1; other site 998088007457 active site 998088007458 motif 2; other site 998088007459 motif 3; other site 998088007460 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 998088007461 anticodon binding site; other site 998088007462 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 998088007463 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 998088007464 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 998088007465 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 998088007466 cytoskeletal protein RodZ; Provisional; Region: PRK10856 998088007467 non-specific DNA binding site [nucleotide binding]; other site 998088007468 salt bridge; other site 998088007469 sequence-specific DNA binding site [nucleotide binding]; other site 998088007470 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 998088007471 TPR repeat; Region: TPR_11; pfam13414 998088007472 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 998088007473 binding surface 998088007474 TPR motif; other site 998088007475 Tetratricopeptide repeat; Region: TPR_12; pfam13424 998088007476 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 998088007477 binding surface 998088007478 TPR motif; other site 998088007479 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 998088007480 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 998088007481 FeS/SAM binding site; other site 998088007482 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 998088007483 active site 998088007484 multimer interface [polypeptide binding]; other site 998088007485 aminopeptidase B; Provisional; Region: PRK05015 998088007486 Peptidase; Region: DUF3663; pfam12404 998088007487 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 998088007488 interface (dimer of trimers) [polypeptide binding]; other site 998088007489 Substrate-binding/catalytic site; other site 998088007490 Zn-binding sites [ion binding]; other site 998088007491 aminopeptidase B; Provisional; Region: PRK05015 998088007492 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 998088007493 interface (dimer of trimers) [polypeptide binding]; other site 998088007494 Substrate-binding/catalytic site; other site 998088007495 Zn-binding sites [ion binding]; other site 998088007496 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 998088007497 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 998088007498 catalytic loop [active] 998088007499 iron binding site [ion binding]; other site 998088007500 chaperone protein HscA; Provisional; Region: hscA; PRK05183 998088007501 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 998088007502 nucleotide binding site [chemical binding]; other site 998088007503 putative NEF/HSP70 interaction site [polypeptide binding]; other site 998088007504 SBD interface [polypeptide binding]; other site 998088007505 co-chaperone HscB; Provisional; Region: hscB; PRK05014 998088007506 DnaJ domain; Region: DnaJ; pfam00226 998088007507 HSP70 interaction site [polypeptide binding]; other site 998088007508 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 998088007509 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 998088007510 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 998088007511 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 998088007512 trimerization site [polypeptide binding]; other site 998088007513 active site 998088007514 cysteine desulfurase; Provisional; Region: PRK14012 998088007515 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 998088007516 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088007517 catalytic residue [active] 998088007518 Transcriptional regulator; Region: Rrf2; cl17282 998088007519 Rrf2 family protein; Region: rrf2_super; TIGR00738 998088007520 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 998088007521 Putative lipid carrier protein [Lipid metabolism]; Region: COG3154 998088007522 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 998088007523 Peptidase family U32; Region: Peptidase_U32; pfam01136 998088007524 putative protease; Provisional; Region: PRK15447 998088007525 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 998088007526 lipoprotein NlpI; Provisional; Region: PRK11189 998088007527 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 998088007528 binding surface 998088007529 TPR motif; other site 998088007530 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 998088007531 active site residue [active] 998088007532 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 998088007533 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 998088007534 Protein export membrane protein; Region: SecD_SecF; pfam02355 998088007535 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 998088007536 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 998088007537 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 998088007538 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 998088007539 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 998088007540 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 998088007541 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 998088007542 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 998088007543 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 998088007544 FOG: CBS domain [General function prediction only]; Region: COG0517 998088007545 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 998088007546 peroxiredoxin; Region: AhpC; TIGR03137 998088007547 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 998088007548 dimer interface [polypeptide binding]; other site 998088007549 decamer (pentamer of dimers) interface [polypeptide binding]; other site 998088007550 catalytic triad [active] 998088007551 peroxidatic and resolving cysteines [active] 998088007552 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 998088007553 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 998088007554 catalytic residue [active] 998088007555 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 998088007556 catalytic residues [active] 998088007557 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088007558 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088007559 Protein of unknown function (DUF541); Region: SIMPL; cl01077 998088007560 CshA-type fibril repeat; Region: CshA_fibril_rpt; TIGR04225 998088007561 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 998088007562 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; cd00198 998088007563 metal ion-dependent adhesion site (MIDAS); other site 998088007564 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; cd00198 998088007565 metal ion-dependent adhesion site (MIDAS); other site 998088007566 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 998088007567 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 998088007568 HAMP domain; Region: HAMP; pfam00672 998088007569 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088007570 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088007571 metal binding site [ion binding]; metal-binding site 998088007572 active site 998088007573 I-site; other site 998088007574 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 998088007575 Predicted transglutaminase-like cysteine proteinase [General function prediction only]; Region: COG3672 998088007576 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 998088007577 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 998088007578 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088007579 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088007580 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 998088007581 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 998088007582 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 998088007583 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 998088007584 Walker A/P-loop; other site 998088007585 ATP binding site [chemical binding]; other site 998088007586 Q-loop/lid; other site 998088007587 ABC transporter signature motif; other site 998088007588 Walker B; other site 998088007589 D-loop; other site 998088007590 H-loop/switch region; other site 998088007591 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 998088007592 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 998088007593 FeS/SAM binding site; other site 998088007594 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 998088007595 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 998088007596 active site 998088007597 dimer interface [polypeptide binding]; other site 998088007598 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 998088007599 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 998088007600 active site 998088007601 FMN binding site [chemical binding]; other site 998088007602 substrate binding site [chemical binding]; other site 998088007603 3Fe-4S cluster binding site [ion binding]; other site 998088007604 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 998088007605 domain interface; other site 998088007606 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 998088007607 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 998088007608 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088007609 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088007610 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 998088007611 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 998088007612 S-adenosylmethionine binding site [chemical binding]; other site 998088007613 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 998088007614 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 998088007615 ATP binding site [chemical binding]; other site 998088007616 Mg++ binding site [ion binding]; other site 998088007617 motif III; other site 998088007618 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 998088007619 nucleotide binding region [chemical binding]; other site 998088007620 ATP-binding site [chemical binding]; other site 998088007621 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 998088007622 FeoC like transcriptional regulator; Region: FeoC; pfam09012 998088007623 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 998088007624 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 998088007625 G1 box; other site 998088007626 GTP/Mg2+ binding site [chemical binding]; other site 998088007627 Switch I region; other site 998088007628 G2 box; other site 998088007629 G3 box; other site 998088007630 Switch II region; other site 998088007631 G4 box; other site 998088007632 G5 box; other site 998088007633 Nucleoside recognition; Region: Gate; pfam07670 998088007634 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 998088007635 Nucleoside recognition; Region: Gate; pfam07670 998088007636 translation initiation factor Sui1; Validated; Region: PRK06824 998088007637 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 998088007638 putative rRNA binding site [nucleotide binding]; other site 998088007639 Predicted membrane protein [Function unknown]; Region: COG2119 998088007640 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 998088007641 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 998088007642 Predicted membrane protein (DUF2157); Region: DUF2157; pfam09925 998088007643 GDYXXLXY protein; Region: GDYXXLXY; pfam14345 998088007644 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007645 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 998088007646 substrate binding pocket [chemical binding]; other site 998088007647 membrane-bound complex binding site; other site 998088007648 hinge residues; other site 998088007649 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 998088007650 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007651 substrate binding pocket [chemical binding]; other site 998088007652 membrane-bound complex binding site; other site 998088007653 hinge residues; other site 998088007654 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007655 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 998088007656 substrate binding pocket [chemical binding]; other site 998088007657 membrane-bound complex binding site; other site 998088007658 hinge residues; other site 998088007659 AAA domain; Region: AAA_21; pfam13304 998088007660 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 998088007661 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 998088007662 active site 998088007663 HIGH motif; other site 998088007664 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 998088007665 KMSKS motif; other site 998088007666 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 998088007667 tRNA binding surface [nucleotide binding]; other site 998088007668 anticodon binding site; other site 998088007669 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 998088007670 substrate binding site [chemical binding]; other site 998088007671 Domain of unknown function (DUF4269); Region: DUF4269; pfam14091 998088007672 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 998088007673 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 998088007674 putative active site [active] 998088007675 putative metal binding site [ion binding]; other site 998088007676 Peptidase M60-like family; Region: M60-like; pfam13402 998088007677 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 998088007678 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 998088007679 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 998088007680 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 998088007681 dimer interface [polypeptide binding]; other site 998088007682 phosphorylation site [posttranslational modification] 998088007683 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 998088007684 ATP binding site [chemical binding]; other site 998088007685 Mg2+ binding site [ion binding]; other site 998088007686 G-X-G motif; other site 998088007687 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 998088007688 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 998088007689 active site 998088007690 phosphorylation site [posttranslational modification] 998088007691 intermolecular recognition site; other site 998088007692 dimerization interface [polypeptide binding]; other site 998088007693 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 998088007694 DNA binding site [nucleotide binding] 998088007695 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 998088007696 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 998088007697 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 998088007698 integrase; Provisional; Region: int; PHA02601 998088007699 Phage HP1 integrase, C-terminal catalytic domain. Bacteriophage HP1 and related integrases are found in eubacteria, plasmids and temperate bacteriophages of the P2 family. They belong to the DNA breaking-rejoining enzyme superfamily, which includes...; Region: HP1_INT_C; cd00797 998088007700 dimer interface [polypeptide binding]; other site 998088007701 active site 998088007702 catalytic residues [active] 998088007703 Int/Topo IB signature motif; other site 998088007704 Domain of unknown function (DUF4209); Region: DUF4209; pfam13910 998088007705 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 998088007706 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 998088007707 Catalytic site [active] 998088007708 Phage regulatory protein CII (CP76); Region: Phage_CP76; pfam06892 998088007709 Ogr/Delta-like zinc finger; Region: Ogr_Delta; pfam04606 998088007710 Helix-turn-helix; Region: HTH_3; pfam01381 998088007711 sequence-specific DNA binding site [nucleotide binding]; other site 998088007712 salt bridge; other site 998088007713 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; pfam05840 998088007714 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 998088007715 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 998088007716 active site 998088007717 DNA binding site [nucleotide binding] 998088007718 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 998088007719 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 998088007720 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 998088007721 Catalytic site [active] 998088007722 Domain of unknown function (DUF4062); Region: DUF4062; pfam13271 998088007723 Phage-related protein [Function unknown]; Region: COG4695; cl01923 998088007724 Phage portal protein; Region: Phage_portal; pfam04860 998088007725 terminase ATPase subunit; Provisional; Region: P; PHA02535 998088007726 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 998088007727 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 998088007728 Phage capsid scaffolding protein (GPO) serine peptidase; Region: Phage_GPO; cl15838 998088007729 capsid protein; Provisional; Region: N; PHA02538 998088007730 terminase endonuclease subunit; Provisional; Region: M; PHA02537 998088007731 Phage small terminase subunit; Region: Phage_term_smal; pfam05944 998088007732 Phage head completion protein (GPL); Region: Phage_GPL; pfam05926 998088007733 Phage Tail Protein X; Region: Phage_tail_X; pfam05489 998088007734 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 998088007735 Protein of unknown function (DUF754); Region: DUF754; pfam05449 998088007736 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 998088007737 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 998088007738 phage lysis regulatory protein, LysB family; Region: phage_LysB; TIGR03495 998088007739 P2 phage tail completion protein R (GpR); Region: P2_Phage_GpR; pfam06891 998088007740 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 998088007741 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 998088007742 Phage-related baseplate assembly protein; Region: Phage_base_V; cl17812 998088007743 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 998088007744 Baseplate J-like protein; Region: Baseplate_J; cl01294 998088007745 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; pfam09684 998088007746 Phage-related tail fibre protein [General function prediction only]; Region: COG5301 998088007747 long tail fiber, proximal subunit; Provisional; Region: 34; PHA02584 998088007748 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; pfam02413 998088007749 major tail sheath protein; Provisional; Region: FI; PHA02560 998088007750 Phage tail tube protein FII; Region: Phage_tube; cl01390 998088007751 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 998088007752 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 998088007753 Phage protein U [General function prediction only]; Region: COG3499 998088007754 tail protein; Provisional; Region: D; PHA02561 998088007755 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 998088007756 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 998088007757 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 998088007758 GIY-YIG motif/motif A; other site 998088007759 active site 998088007760 catalytic site [active] 998088007761 putative DNA binding site [nucleotide binding]; other site 998088007762 metal binding site [ion binding]; metal-binding site 998088007763 UvrB/uvrC motif; Region: UVR; pfam02151 998088007764 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 998088007765 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 998088007766 response regulator; Provisional; Region: PRK09483 998088007767 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 998088007768 active site 998088007769 phosphorylation site [posttranslational modification] 998088007770 intermolecular recognition site; other site 998088007771 dimerization interface [polypeptide binding]; other site 998088007772 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 998088007773 DNA binding residues [nucleotide binding] 998088007774 dimerization interface [polypeptide binding]; other site 998088007775 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 998088007776 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 998088007777 Ligand binding site; other site 998088007778 oligomer interface; other site 998088007779 Trm112p-like protein; Region: Trm112p; cl01066 998088007780 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 998088007781 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 998088007782 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 998088007783 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 998088007784 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 998088007785 Walker A/P-loop; other site 998088007786 ATP binding site [chemical binding]; other site 998088007787 Q-loop/lid; other site 998088007788 ABC transporter signature motif; other site 998088007789 Walker B; other site 998088007790 D-loop; other site 998088007791 H-loop/switch region; other site 998088007792 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 998088007793 Competence protein; Region: Competence; pfam03772 998088007794 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 998088007795 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 998088007796 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 998088007797 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 998088007798 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 998088007799 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088007800 homodimer interface [polypeptide binding]; other site 998088007801 catalytic residue [active] 998088007802 transcriptional regulator HdfR; Provisional; Region: PRK03601 998088007803 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088007804 LysR substrate binding domain; Region: LysR_substrate; pfam03466 998088007805 hypothetical protein; Provisional; Region: PRK11027 998088007806 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 998088007807 secondary substrate binding site; other site 998088007808 primary substrate binding site; other site 998088007809 inhibition loop; other site 998088007810 dimerization interface [polypeptide binding]; other site 998088007811 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 998088007812 Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins; Region: GDPD_EcGlpQ_like; cd08600 998088007813 active site 998088007814 catalytic site [active] 998088007815 metal binding site [ion binding]; metal-binding site 998088007816 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 998088007817 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 998088007818 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 998088007819 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 998088007820 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 998088007821 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 998088007822 putative substrate translocation pore; other site 998088007823 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 998088007824 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 998088007825 amphipathic channel; other site 998088007826 Asn-Pro-Ala signature motifs; other site 998088007827 glycerol kinase; Provisional; Region: glpK; PRK00047 998088007828 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 998088007829 N- and C-terminal domain interface [polypeptide binding]; other site 998088007830 active site 998088007831 MgATP binding site [chemical binding]; other site 998088007832 catalytic site [active] 998088007833 metal binding site [ion binding]; metal-binding site 998088007834 glycerol binding site [chemical binding]; other site 998088007835 homotetramer interface [polypeptide binding]; other site 998088007836 homodimer interface [polypeptide binding]; other site 998088007837 FBP binding site [chemical binding]; other site 998088007838 protein IIAGlc interface [polypeptide binding]; other site 998088007839 Cache domain; Region: Cache_1; pfam02743 998088007840 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 998088007841 dimerization interface [polypeptide binding]; other site 998088007842 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088007843 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088007844 dimer interface [polypeptide binding]; other site 998088007845 putative CheW interface [polypeptide binding]; other site 998088007846 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088007847 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088007848 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 998088007849 dimerization interface [polypeptide binding]; other site 998088007850 Uncharacterized conserved protein [Function unknown]; Region: COG1359 998088007851 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 998088007852 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 998088007853 active site 998088007854 catalytic tetrad [active] 998088007855 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 998088007856 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 998088007857 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 998088007858 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 998088007859 putative substrate translocation pore; other site 998088007860 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 998088007861 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 998088007862 Predicted membrane protein [Function unknown]; Region: COG2259 998088007863 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 998088007864 hypothetical protein; Provisional; Region: PRK05409 998088007865 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 998088007866 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 998088007867 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 998088007868 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 998088007869 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 998088007870 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 998088007871 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088007872 DNA-binding site [nucleotide binding]; DNA binding site 998088007873 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 998088007874 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088007875 homodimer interface [polypeptide binding]; other site 998088007876 catalytic residue [active] 998088007877 Protein of unknown function (DUF533); Region: DUF533; pfam04391 998088007878 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 998088007879 putative metal binding site [ion binding]; other site 998088007880 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 998088007881 Protein of unknown function (DUF2496); Region: DUF2496; cl11670 998088007882 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088007883 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088007884 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 998088007885 dimerization interface [polypeptide binding]; other site 998088007886 putative cyanate transporter; Provisional; Region: cynX; PRK09705 998088007887 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 998088007888 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 998088007889 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 998088007890 RNA binding surface [nucleotide binding]; other site 998088007891 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 998088007892 probable active site [active] 998088007893 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 998088007894 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 998088007895 dimer interface [polypeptide binding]; other site 998088007896 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 998088007897 metal binding site [ion binding]; metal-binding site 998088007898 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 998088007899 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 998088007900 DNA binding site [nucleotide binding] 998088007901 substrate interaction site [chemical binding]; other site 998088007902 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 998088007903 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 998088007904 additional DNA contacts [nucleotide binding]; other site 998088007905 mismatch recognition site; other site 998088007906 active site 998088007907 zinc binding site [ion binding]; other site 998088007908 DNA intercalation site [nucleotide binding]; other site 998088007909 electron transport complex protein RsxA; Provisional; Region: PRK05151 998088007910 ferredoxin; Provisional; Region: PRK08764 998088007911 Putative Fe-S cluster; Region: FeS; pfam04060 998088007912 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 998088007913 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 998088007914 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 998088007915 SLBB domain; Region: SLBB; pfam10531 998088007916 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 998088007917 electron transport complex protein RnfD; Reviewed; Region: rnfD; PRK00816 998088007918 electron transport complex protein RnfG; Validated; Region: PRK01908 998088007919 electron transport complex RsxE subunit; Provisional; Region: PRK12405 998088007920 endonuclease III; Provisional; Region: PRK10702 998088007921 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 998088007922 minor groove reading motif; other site 998088007923 helix-hairpin-helix signature motif; other site 998088007924 substrate binding pocket [chemical binding]; other site 998088007925 active site 998088007926 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 998088007927 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 998088007928 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 998088007929 dimer interface [polypeptide binding]; other site 998088007930 active site 998088007931 glutathione binding site [chemical binding]; other site 998088007932 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 998088007933 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088007934 ligand binding site [chemical binding]; other site 998088007935 Winged helix-turn helix; Region: HTH_29; pfam13551 998088007936 Helix-turn-helix domain; Region: HTH_28; pfam13518 998088007937 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 998088007938 Integrase core domain; Region: rve; pfam00665 998088007939 Integrase core domain; Region: rve_3; pfam13683 998088007940 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 998088007941 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 998088007942 trimer interface [polypeptide binding]; other site 998088007943 eyelet of channel; other site 998088007944 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 998088007945 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 998088007946 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 998088007947 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 998088007948 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 998088007949 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 998088007950 putative active site [active] 998088007951 Zn binding site [ion binding]; other site 998088007952 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 998088007953 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 998088007954 GTP/Mg2+ binding site [chemical binding]; other site 998088007955 G4 box; other site 998088007956 G5 box; other site 998088007957 G1 box; other site 998088007958 Switch I region; other site 998088007959 G2 box; other site 998088007960 G3 box; other site 998088007961 Switch II region; other site 998088007962 Alkaline phosphatase [Inorganic ion transport and metabolism]; Region: PhoA; COG1785 998088007963 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 998088007964 dimer interface [polypeptide binding]; other site 998088007965 active site 998088007966 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 998088007967 dimer interface [polypeptide binding]; other site 998088007968 Alkaline phosphatase homologues; Region: alkPPc; smart00098 998088007969 active site 998088007970 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 998088007971 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088007972 substrate binding pocket [chemical binding]; other site 998088007973 membrane-bound complex binding site; other site 998088007974 hinge residues; other site 998088007975 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 998088007976 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 998088007977 DNA-binding transcriptional activator UhpA; Provisional; Region: PRK10360 998088007978 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 998088007979 active site 998088007980 phosphorylation site [posttranslational modification] 998088007981 intermolecular recognition site; other site 998088007982 dimerization interface [polypeptide binding]; other site 998088007983 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 998088007984 DNA binding residues [nucleotide binding] 998088007985 dimerization interface [polypeptide binding]; other site 998088007986 sensory histidine kinase UhpB; Provisional; Region: PRK11644 998088007987 MASE1; Region: MASE1; cl17823 998088007988 Histidine kinase; Region: HisKA_3; pfam07730 998088007989 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 998088007990 ATP binding site [chemical binding]; other site 998088007991 Mg2+ binding site [ion binding]; other site 998088007992 G-X-G motif; other site 998088007993 regulatory protein UhpC; Provisional; Region: PRK11663 998088007994 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 998088007995 putative substrate translocation pore; other site 998088007996 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088007997 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088007998 metal binding site [ion binding]; metal-binding site 998088007999 active site 998088008000 I-site; other site 998088008001 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 998088008002 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088008003 substrate binding pocket [chemical binding]; other site 998088008004 membrane-bound complex binding site; other site 998088008005 hinge residues; other site 998088008006 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088008007 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 998088008008 dimer interface [polypeptide binding]; other site 998088008009 conserved gate region; other site 998088008010 putative PBP binding loops; other site 998088008011 ABC-ATPase subunit interface; other site 998088008012 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 998088008013 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 998088008014 Walker A/P-loop; other site 998088008015 ATP binding site [chemical binding]; other site 998088008016 Q-loop/lid; other site 998088008017 ABC transporter signature motif; other site 998088008018 Walker B; other site 998088008019 D-loop; other site 998088008020 H-loop/switch region; other site 998088008021 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 998088008022 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088008023 substrate binding pocket [chemical binding]; other site 998088008024 membrane-bound complex binding site; other site 998088008025 hinge residues; other site 998088008026 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 998088008027 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 998088008028 transporter, basic amino acid/polyamine antiporter (APA) family; Region: 2A0302; TIGR00905 998088008029 Spore germination protein; Region: Spore_permease; cl17796 998088008030 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; COG2040 998088008031 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 998088008032 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 998088008033 Domain of unknown function DUF21; Region: DUF21; pfam01595 998088008034 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 998088008035 Transporter associated domain; Region: CorC_HlyC; smart01091 998088008036 transcriptional regulator PhoU; Provisional; Region: PRK11115 998088008037 PhoU domain; Region: PhoU; pfam01895 998088008038 PhoU domain; Region: PhoU; pfam01895 998088008039 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 998088008040 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 998088008041 Walker A/P-loop; other site 998088008042 ATP binding site [chemical binding]; other site 998088008043 Q-loop/lid; other site 998088008044 ABC transporter signature motif; other site 998088008045 Walker B; other site 998088008046 D-loop; other site 998088008047 H-loop/switch region; other site 998088008048 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 998088008049 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 998088008050 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 998088008051 dimer interface [polypeptide binding]; other site 998088008052 conserved gate region; other site 998088008053 putative PBP binding loops; other site 998088008054 ABC-ATPase subunit interface; other site 998088008055 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 998088008056 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 998088008057 conserved gate region; other site 998088008058 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 998088008059 ABC-ATPase subunit interface; other site 998088008060 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 998088008061 nucleoside/Zn binding site; other site 998088008062 dimer interface [polypeptide binding]; other site 998088008063 catalytic motif [active] 998088008064 malate synthase A; Region: malate_syn_A; TIGR01344 998088008065 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 998088008066 active site 998088008067 isocitrate lyase; Provisional; Region: PRK15063 998088008068 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 998088008069 tetramer interface [polypeptide binding]; other site 998088008070 active site 998088008071 Mg2+/Mn2+ binding site [ion binding]; other site 998088008072 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 998088008073 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 998088008074 Walker A motif; other site 998088008075 ATP binding site [chemical binding]; other site 998088008076 Walker B motif; other site 998088008077 arginine finger; other site 998088008078 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3249 998088008079 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 998088008080 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 998088008081 active site 998088008082 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 998088008083 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 998088008084 dimerization interface [polypeptide binding]; other site 998088008085 putative ATP binding site [chemical binding]; other site 998088008086 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 998088008087 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 998088008088 active site 998088008089 substrate binding site [chemical binding]; other site 998088008090 cosubstrate binding site; other site 998088008091 catalytic site [active] 998088008092 Uncharacterized conserved protein [Function unknown]; Region: COG0327 998088008093 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 998088008094 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 998088008095 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 998088008096 active site 998088008097 phosphorylation site [posttranslational modification] 998088008098 intermolecular recognition site; other site 998088008099 dimerization interface [polypeptide binding]; other site 998088008100 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 998088008101 Walker A motif; other site 998088008102 ATP binding site [chemical binding]; other site 998088008103 Walker B motif; other site 998088008104 arginine finger; other site 998088008105 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 998088008106 PAS domain; Region: PAS_8; pfam13188 998088008107 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088008108 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 998088008109 dimer interface [polypeptide binding]; other site 998088008110 phosphorylation site [posttranslational modification] 998088008111 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 998088008112 ATP binding site [chemical binding]; other site 998088008113 G-X-G motif; other site 998088008114 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 998088008115 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 998088008116 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 998088008117 Walker A motif; other site 998088008118 ATP binding site [chemical binding]; other site 998088008119 Walker B motif; other site 998088008120 arginine finger; other site 998088008121 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 998088008122 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 998088008123 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 998088008124 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 998088008125 ACT domain; Region: ACT_6; pfam13740 998088008126 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 998088008127 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 998088008128 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 998088008129 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 998088008130 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 998088008131 domain interface [polypeptide binding]; other site 998088008132 active site 998088008133 catalytic site [active] 998088008134 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 998088008135 domain interface [polypeptide binding]; other site 998088008136 active site 998088008137 catalytic site [active] 998088008138 exopolyphosphatase; Provisional; Region: PRK10854 998088008139 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 998088008140 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 998088008141 MgtE intracellular N domain; Region: MgtE_N; smart00924 998088008142 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 998088008143 Divalent cation transporter; Region: MgtE; pfam01769 998088008144 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 998088008145 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 998088008146 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK05683 998088008147 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 998088008148 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 998088008149 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 998088008150 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 998088008151 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 998088008152 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 998088008153 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 998088008154 Flagellar L-ring protein; Region: FlgH; pfam02107 998088008155 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 998088008156 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 998088008157 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 998088008158 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 998088008159 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 998088008160 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 998088008161 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 998088008162 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 998088008163 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 998088008164 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 998088008165 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 998088008166 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 998088008167 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12631 998088008168 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 998088008169 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 998088008170 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12625 998088008171 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 998088008172 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 998088008173 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 998088008174 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 998088008175 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 998088008176 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088008177 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 998088008178 active site 998088008179 phosphorylation site [posttranslational modification] 998088008180 intermolecular recognition site; other site 998088008181 dimerization interface [polypeptide binding]; other site 998088008182 SAF-like; Region: SAF_2; pfam13144 998088008183 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 998088008184 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 998088008185 FlgN protein; Region: FlgN; pfam05130 998088008186 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 998088008187 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 998088008188 active site 998088008189 metal binding site [ion binding]; metal-binding site 998088008190 homotetramer interface [polypeptide binding]; other site 998088008191 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 998088008192 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 998088008193 peptide binding site [polypeptide binding]; other site 998088008194 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088008195 EamA-like transporter family; Region: EamA; pfam00892 998088008196 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 998088008197 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 998088008198 RNA binding surface [nucleotide binding]; other site 998088008199 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 998088008200 active site 998088008201 uracil binding [chemical binding]; other site 998088008202 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 998088008203 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 998088008204 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088008205 Zn2+ binding site [ion binding]; other site 998088008206 Mg2+ binding site [ion binding]; other site 998088008207 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 998088008208 active site 998088008209 intersubunit interactions; other site 998088008210 catalytic residue [active] 998088008211 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 998088008212 FeS/SAM binding site; other site 998088008213 glycyl radical enzyme, PFL2/glycerol dehydratase family; Region: PFL2-3; TIGR01774 998088008214 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 998088008215 dimer interface [polypeptide binding]; other site 998088008216 active site 998088008217 glycine loop; other site 998088008218 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 998088008219 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 998088008220 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 998088008221 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 998088008222 EamA-like transporter family; Region: EamA; pfam00892 998088008223 EamA-like transporter family; Region: EamA; pfam00892 998088008224 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 998088008225 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 998088008226 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 998088008227 Phosphate-starvation-inducible E; Region: PsiE; cl01264 998088008228 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 998088008229 DNA-binding site [nucleotide binding]; DNA binding site 998088008230 RNA-binding motif; other site 998088008231 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 998088008232 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 998088008233 E3 interaction surface; other site 998088008234 lipoyl attachment site [posttranslational modification]; other site 998088008235 e3 binding domain; Region: E3_binding; pfam02817 998088008236 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 998088008237 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 998088008238 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 998088008239 alpha subunit interface [polypeptide binding]; other site 998088008240 TPP binding site [chemical binding]; other site 998088008241 heterodimer interface [polypeptide binding]; other site 998088008242 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 998088008243 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 998088008244 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 998088008245 tetramer interface [polypeptide binding]; other site 998088008246 TPP-binding site [chemical binding]; other site 998088008247 heterodimer interface [polypeptide binding]; other site 998088008248 phosphorylation loop region [posttranslational modification] 998088008249 enterobactin synthase subunit F; Provisional; Region: entF; PRK10252 998088008250 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 998088008251 acyl-activating enzyme (AAE) consensus motif; other site 998088008252 AMP binding site [chemical binding]; other site 998088008253 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 998088008254 2,3-dihydroxybenzoate-2,3-dehydrogenase; Validated; Region: PRK08220 998088008255 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008256 NAD(P) binding site [chemical binding]; other site 998088008257 active site 998088008258 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 998088008259 Isochorismatase family; Region: Isochorismatase; pfam00857 998088008260 catalytic triad [active] 998088008261 conserved cis-peptide bond; other site 998088008262 Aryl carrier domain [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3433 998088008263 enterobactin synthase subunit E; Provisional; Region: entE; PRK10946 998088008264 2,3-dihydroxybenzoate-AMP ligase; Region: 23DHB-AMP_lg; cd05920 998088008265 acyl-activating enzyme (AAE) consensus motif; other site 998088008266 active site 998088008267 AMP binding site [chemical binding]; other site 998088008268 substrate binding site [chemical binding]; other site 998088008269 isochorismate synthase DhbC; Validated; Region: PRK06923 998088008270 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 998088008271 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 998088008272 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 998088008273 N-terminal plug; other site 998088008274 ligand-binding site [chemical binding]; other site 998088008275 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 998088008276 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 998088008277 Transcriptional regulators [Transcription]; Region: PurR; COG1609 998088008278 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088008279 DNA binding site [nucleotide binding] 998088008280 domain linker motif; other site 998088008281 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 998088008282 dimerization interface (closed form) [polypeptide binding]; other site 998088008283 ligand binding site [chemical binding]; other site 998088008284 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 998088008285 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 998088008286 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088008287 catalytic residue [active] 998088008288 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 998088008289 PAS domain; Region: PAS_9; pfam13426 998088008290 putative active site [active] 998088008291 heme pocket [chemical binding]; other site 998088008292 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088008293 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088008294 metal binding site [ion binding]; metal-binding site 998088008295 active site 998088008296 I-site; other site 998088008297 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 998088008298 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 998088008299 30S subunit binding site; other site 998088008300 Ribosomal S4P (gammaproteobacterial); Region: Ribosomal_S4Pg; pfam11993 998088008301 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 998088008302 Family of unknown function (DUF490); Region: DUF490; pfam04357 998088008303 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 998088008304 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 998088008305 Surface antigen; Region: Bac_surface_Ag; pfam01103 998088008306 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 998088008307 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 998088008308 Uncharacterized conserved protein [Function unknown]; Region: COG2128 998088008309 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 998088008310 Uncharacterized conserved protein [Function unknown]; Region: COG0398 998088008311 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 998088008312 mercuric reductase; Validated; Region: PRK06370 998088008313 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088008314 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088008315 hypothetical protein; Provisional; Region: PRK11622 998088008316 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4134 998088008317 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4135 998088008318 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4136 998088008319 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088008320 Walker A/P-loop; other site 998088008321 ATP binding site [chemical binding]; other site 998088008322 Q-loop/lid; other site 998088008323 ABC transporter signature motif; other site 998088008324 Walker B; other site 998088008325 D-loop; other site 998088008326 H-loop/switch region; other site 998088008327 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 998088008328 Transglycosylase SLT domain; Region: SLT_2; pfam13406 998088008329 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 998088008330 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088008331 MarR family; Region: MarR_2; cl17246 998088008332 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 998088008333 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 998088008334 EamA-like transporter family; Region: EamA; pfam00892 998088008335 phosphoglucomutase; Validated; Region: PRK07564 998088008336 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl...; Region: PGM_like3; cd05801 998088008337 active site 998088008338 substrate binding site [chemical binding]; other site 998088008339 metal binding site [ion binding]; metal-binding site 998088008340 SeqA protein; Region: SeqA; pfam03925 998088008341 acyl-CoA esterase; Provisional; Region: PRK10673 998088008342 PGAP1-like protein; Region: PGAP1; pfam07819 998088008343 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 998088008344 LexA regulated protein; Provisional; Region: PRK11675 998088008345 flavodoxin FldA; Validated; Region: PRK09267 998088008346 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 998088008347 active site 2 [active] 998088008348 active site 1 [active] 998088008349 ferric uptake regulator; Provisional; Region: fur; PRK09462 998088008350 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 998088008351 metal binding site 2 [ion binding]; metal-binding site 998088008352 putative DNA binding helix; other site 998088008353 metal binding site 1 [ion binding]; metal-binding site 998088008354 dimer interface [polypeptide binding]; other site 998088008355 structural Zn2+ binding site [ion binding]; other site 998088008356 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 998088008357 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 998088008358 active site 998088008359 HIGH motif; other site 998088008360 nucleotide binding site [chemical binding]; other site 998088008361 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 998088008362 KMSKS motif; other site 998088008363 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 998088008364 Putative carbohydrate binding domain; Region: CHB_HEX; smart01081 998088008365 N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism]; Region: Chb; COG3525 998088008366 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a...; Region: GH20_Sm-chitobiase-like; cd06569 998088008367 active site 998088008368 C-terminal Early set domain associated with the catalytic domain of chitobiase (also called N-acetylglucosaminidase); Region: E_set_Chitobiase_C; cd02847 998088008369 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 998088008370 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 998088008371 PTS_IIB, PTS system, glucose/sucrose specific IIB 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_IIB_glc; cd00212 998088008372 active site turn [active] 998088008373 phosphorylation site [posttranslational modification] 998088008374 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 998088008375 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 998088008376 active site 998088008377 trimer interface [polypeptide binding]; other site 998088008378 allosteric site; other site 998088008379 active site lid [active] 998088008380 hexamer (dimer of trimers) interface [polypeptide binding]; other site 998088008381 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 998088008382 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 998088008383 active site 998088008384 dimer interface [polypeptide binding]; other site 998088008385 MarR family; Region: MarR_2; cl17246 998088008386 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 998088008387 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 998088008388 nucleotide binding site [chemical binding]; other site 998088008389 putative metal dependent hydrolase; Provisional; Region: PRK11598 998088008390 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 998088008391 Sulfatase; Region: Sulfatase; pfam00884 998088008392 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 998088008393 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 998088008394 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088008395 Zn2+ binding site [ion binding]; other site 998088008396 Mg2+ binding site [ion binding]; other site 998088008397 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 998088008398 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 998088008399 GAF domain; Region: GAF; pfam01590 998088008400 Histidine kinase; Region: His_kinase; pfam06580 998088008401 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 998088008402 ATP binding site [chemical binding]; other site 998088008403 Mg2+ binding site [ion binding]; other site 998088008404 G-X-G motif; other site 998088008405 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 998088008406 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 998088008407 active site 998088008408 phosphorylation site [posttranslational modification] 998088008409 intermolecular recognition site; other site 998088008410 dimerization interface [polypeptide binding]; other site 998088008411 LytTr DNA-binding domain; Region: LytTR; smart00850 998088008412 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 998088008413 Carbon starvation protein CstA; Region: CstA; pfam02554 998088008414 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 998088008415 Protein of unknown function (DUF3302); Region: DUF3302; pfam11742 998088008416 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088008417 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088008418 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088008419 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 998088008420 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 998088008421 ATP binding site [chemical binding]; other site 998088008422 putative Mg++ binding site [ion binding]; other site 998088008423 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 998088008424 nucleotide binding region [chemical binding]; other site 998088008425 ATP-binding site [chemical binding]; other site 998088008426 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 998088008427 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 998088008428 GSH binding site [chemical binding]; other site 998088008429 catalytic residues [active] 998088008430 hypothetical protein; Provisional; Region: PRK05421 998088008431 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 998088008432 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008433 NAD(P) binding site [chemical binding]; other site 998088008434 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 998088008435 active site 998088008436 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 998088008437 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 998088008438 dimer interface [polypeptide binding]; other site 998088008439 PYR/PP interface [polypeptide binding]; other site 998088008440 TPP binding site [chemical binding]; other site 998088008441 substrate binding site [chemical binding]; other site 998088008442 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 998088008443 Domain of unknown function; Region: EKR; smart00890 998088008444 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 998088008445 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 998088008446 TPP-binding site [chemical binding]; other site 998088008447 dimer interface [polypeptide binding]; other site 998088008448 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 998088008449 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 998088008450 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088008451 4Fe-4S binding domain; Region: Fer4; pfam00037 998088008452 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 998088008453 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088008454 substrate binding pocket [chemical binding]; other site 998088008455 membrane-bound complex binding site; other site 998088008456 hinge residues; other site 998088008457 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 998088008458 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 998088008459 MOSC domain; Region: MOSC; pfam03473 998088008460 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 998088008461 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 998088008462 FAD binding pocket [chemical binding]; other site 998088008463 FAD binding motif [chemical binding]; other site 998088008464 phosphate binding motif [ion binding]; other site 998088008465 beta-alpha-beta structure motif; other site 998088008466 NAD binding pocket [chemical binding]; other site 998088008467 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 998088008468 catalytic loop [active] 998088008469 iron binding site [ion binding]; other site 998088008470 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088008471 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088008472 dimer interface [polypeptide binding]; other site 998088008473 putative CheW interface [polypeptide binding]; other site 998088008474 heat shock protein HtpX; Provisional; Region: PRK05457 998088008475 AAA domain; Region: AAA_26; pfam13500 998088008476 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 998088008477 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 998088008478 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 998088008479 S-adenosylmethionine binding site [chemical binding]; other site 998088008480 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 998088008481 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 998088008482 substrate-cofactor binding pocket; other site 998088008483 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008484 catalytic residue [active] 998088008485 biotin synthase; Provisional; Region: PRK15108 998088008486 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 998088008487 FeS/SAM binding site; other site 998088008488 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 998088008489 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 998088008490 adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated; Region: PRK07986 998088008491 inhibitor-cofactor binding pocket; inhibition site 998088008492 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008493 catalytic residue [active] 998088008494 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 998088008495 dimerization interface [polypeptide binding]; other site 998088008496 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 998088008497 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 998088008498 putative dimer interface [polypeptide binding]; other site 998088008499 putative anticodon binding site; other site 998088008500 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 998088008501 homodimer interface [polypeptide binding]; other site 998088008502 motif 1; other site 998088008503 motif 2; other site 998088008504 active site 998088008505 motif 3; other site 998088008506 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088008507 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 998088008508 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK12489 998088008509 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_IV; cd01994 998088008510 Ligand Binding Site [chemical binding]; other site 998088008511 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 998088008512 hypothetical protein; Provisional; Region: PRK07338 998088008513 metal binding site [ion binding]; metal-binding site 998088008514 dimer interface [polypeptide binding]; other site 998088008515 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; COG3069 998088008516 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 998088008517 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 998088008518 ArsC family; Region: ArsC; pfam03960 998088008519 putative catalytic residues [active] 998088008520 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 998088008521 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 998088008522 metal binding site [ion binding]; metal-binding site 998088008523 dimer interface [polypeptide binding]; other site 998088008524 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 998088008525 potassium/proton antiporter; Reviewed; Region: PRK05326 998088008526 TrkA-C domain; Region: TrkA_C; pfam02080 998088008527 Transporter associated domain; Region: CorC_HlyC; smart01091 998088008528 beta-N-acetylglucosaminidase; Region: NAGidase; pfam07555 998088008529 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 998088008530 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 998088008531 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088008532 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 998088008533 dimerization interface [polypeptide binding]; other site 998088008534 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088008535 dimer interface [polypeptide binding]; other site 998088008536 putative CheW interface [polypeptide binding]; other site 998088008537 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 998088008538 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; pfam09904 998088008539 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 998088008540 active site 998088008541 tetramer interface [polypeptide binding]; other site 998088008542 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 998088008543 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 998088008544 active site 998088008545 uridine phosphorylase; Provisional; Region: PRK11178 998088008546 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 998088008547 putative alcohol dehydrogenase; Provisional; Region: PRK09860 998088008548 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 998088008549 dimer interface [polypeptide binding]; other site 998088008550 active site 998088008551 metal binding site [ion binding]; metal-binding site 998088008552 von Willebrand factor (vWF) type A domain; Region: VWA; smart00327 998088008553 metal ion-dependent adhesion site (MIDAS); other site 998088008554 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 998088008555 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 998088008556 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 998088008557 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 998088008558 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 998088008559 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 998088008560 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 998088008561 ATP binding site [chemical binding]; other site 998088008562 Walker A motif; other site 998088008563 hexamer interface [polypeptide binding]; other site 998088008564 Walker B motif; other site 998088008565 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 998088008566 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 998088008567 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 998088008568 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 998088008569 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 998088008570 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 998088008571 Flp/Fap pilin component; Region: Flp_Fap; cl01585 998088008572 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 998088008573 Interdomain contacts; other site 998088008574 Cytokine receptor motif; other site 998088008575 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 998088008576 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 998088008577 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 998088008578 NADH(P)-binding; Region: NAD_binding_10; pfam13460 998088008579 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 998088008580 NAD binding site [chemical binding]; other site 998088008581 active site 998088008582 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 998088008583 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088008584 catalytic residue [active] 998088008585 lipoate-protein ligase A; Provisional; Region: lplA; PRK03822 998088008586 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 998088008587 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 998088008588 NMT1/THI5 like; Region: NMT1; pfam09084 998088008589 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 998088008590 substrate binding pocket [chemical binding]; other site 998088008591 membrane-bound complex binding site; other site 998088008592 PAS domain S-box; Region: sensory_box; TIGR00229 998088008593 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 998088008594 putative active site [active] 998088008595 heme pocket [chemical binding]; other site 998088008596 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088008597 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088008598 metal binding site [ion binding]; metal-binding site 998088008599 active site 998088008600 I-site; other site 998088008601 Hemerythrin; Region: Hemerythrin; cd12107 998088008602 Fe binding site [ion binding]; other site 998088008603 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 998088008604 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088008605 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088008606 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 998088008607 FtsX-like permease family; Region: FtsX; pfam02687 998088008608 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 998088008609 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 998088008610 Walker A/P-loop; other site 998088008611 ATP binding site [chemical binding]; other site 998088008612 Q-loop/lid; other site 998088008613 ABC transporter signature motif; other site 998088008614 Walker B; other site 998088008615 D-loop; other site 998088008616 H-loop/switch region; other site 998088008617 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088008618 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088008619 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 998088008620 Protein export membrane protein; Region: SecD_SecF; cl14618 998088008621 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088008622 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 998088008623 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 998088008624 Predicted transporter component [General function prediction only]; Region: COG2391 998088008625 Sulphur transport; Region: Sulf_transp; pfam04143 998088008626 Predicted transporter component [General function prediction only]; Region: COG2391 998088008627 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 998088008628 putative DNA binding site [nucleotide binding]; other site 998088008629 putative Zn2+ binding site [ion binding]; other site 998088008630 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 998088008631 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 998088008632 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 998088008633 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 998088008634 MgtC family; Region: MgtC; pfam02308 998088008635 D-fructose-responsive transcription factor; Region: fruct_sucro_rep; TIGR02417 998088008636 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088008637 DNA binding site [nucleotide binding] 998088008638 domain linker motif; other site 998088008639 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 998088008640 dimerization interface [polypeptide binding]; other site 998088008641 ligand binding site [chemical binding]; other site 998088008642 sucrose-6-phosphate hydrolase; Region: scrB_fam; TIGR01322 998088008643 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 998088008644 substrate binding [chemical binding]; other site 998088008645 active site 998088008646 PTS system, sucrose-specific IIBC component; Region: PTS-II-BC-sucr; TIGR01996 998088008647 PTS_IIB, PTS system, glucose/sucrose specific IIB 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_IIB_glc; cd00212 998088008648 active site turn [active] 998088008649 phosphorylation site [posttranslational modification] 998088008650 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 998088008651 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 998088008652 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 998088008653 putative substrate binding site [chemical binding]; other site 998088008654 putative ATP binding site [chemical binding]; other site 998088008655 The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel...; Region: Maltoporin-like; cd01346 998088008656 trimer interface; other site 998088008657 sugar binding site [chemical binding]; other site 998088008658 chaperone protein DnaJ; Provisional; Region: PRK10767 998088008659 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 998088008660 HSP70 interaction site [polypeptide binding]; other site 998088008661 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 998088008662 substrate binding site [polypeptide binding]; other site 998088008663 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 998088008664 Zn binding sites [ion binding]; other site 998088008665 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 998088008666 dimer interface [polypeptide binding]; other site 998088008667 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 998088008668 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 998088008669 nucleotide binding site [chemical binding]; other site 998088008670 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 998088008671 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 998088008672 dimer interface [polypeptide binding]; other site 998088008673 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 998088008674 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03378 998088008675 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 998088008676 recombination and repair protein; Provisional; Region: PRK10869 998088008677 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 998088008678 Walker A/P-loop; other site 998088008679 ATP binding site [chemical binding]; other site 998088008680 Q-loop/lid; other site 998088008681 Protein of unknown function (DUF935); Region: DUF935; pfam06074 998088008682 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 998088008683 Q-loop/lid; other site 998088008684 ABC transporter signature motif; other site 998088008685 Walker B; other site 998088008686 D-loop; other site 998088008687 H-loop/switch region; other site 998088008688 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 998088008689 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 998088008690 DHHA2 domain; Region: DHHA2; pfam02833 998088008691 macrolide transporter subunit MacA; Provisional; Region: PRK11578 998088008692 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088008693 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088008694 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 998088008695 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 998088008696 Walker A/P-loop; other site 998088008697 ATP binding site [chemical binding]; other site 998088008698 Q-loop/lid; other site 998088008699 ABC transporter signature motif; other site 998088008700 Walker B; other site 998088008701 D-loop; other site 998088008702 H-loop/switch region; other site 998088008703 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 998088008704 FtsX-like permease family; Region: FtsX; pfam02687 998088008705 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 998088008706 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 998088008707 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 998088008708 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 998088008709 O-Antigen ligase; Region: Wzy_C; pfam04932 998088008710 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 998088008711 LPS O-antigen length regulator; Provisional; Region: PRK10381 998088008712 Chain length determinant protein; Region: Wzz; pfam02706 998088008713 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 998088008714 putative transposase OrfB; Reviewed; Region: PHA02517 998088008715 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 998088008716 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 998088008717 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 998088008718 NAD(P) binding site [chemical binding]; other site 998088008719 homodimer interface [polypeptide binding]; other site 998088008720 substrate binding site [chemical binding]; other site 998088008721 active site 998088008722 Bacterial sugar transferase; Region: Bac_transf; pfam02397 998088008723 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 998088008724 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 998088008725 putative NAD(P) binding site [chemical binding]; other site 998088008726 active site 998088008727 putative substrate binding site [chemical binding]; other site 998088008728 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 998088008729 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 998088008730 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 998088008731 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 998088008732 active site 998088008733 homodimer interface [polypeptide binding]; other site 998088008734 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008735 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 998088008736 NAD(P) binding site [chemical binding]; other site 998088008737 active site 998088008738 dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfbC; COG1898 998088008739 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 998088008740 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 998088008741 NAD(P) binding site [chemical binding]; other site 998088008742 homodimer interface [polypeptide binding]; other site 998088008743 substrate binding site [chemical binding]; other site 998088008744 active site 998088008745 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 998088008746 imidazole glycerol phosphate synthase subunit HisF; Provisional; Region: PRK01033 998088008747 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 998088008748 substrate binding site [chemical binding]; other site 998088008749 glutamase interaction surface [polypeptide binding]; other site 998088008750 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 998088008751 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 998088008752 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_III; cd01996 998088008753 Ligand Binding Site [chemical binding]; other site 998088008754 flagellin modification protein A; Provisional; Region: PRK09186 998088008755 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008756 NAD(P) binding site [chemical binding]; other site 998088008757 active site 998088008758 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 998088008759 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 998088008760 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 998088008761 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 998088008762 FOG: CBS domain [General function prediction only]; Region: COG0517 998088008763 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 998088008764 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_2; cd06426 998088008765 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 998088008766 Substrate binding site; other site 998088008767 metal-binding site 998088008768 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 998088008769 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 998088008770 putative trimer interface [polypeptide binding]; other site 998088008771 putative CoA binding site [chemical binding]; other site 998088008772 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 998088008773 NeuB family; Region: NeuB; pfam03102 998088008774 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 998088008775 NeuB binding interface [polypeptide binding]; other site 998088008776 putative substrate binding site [chemical binding]; other site 998088008777 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 998088008778 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 998088008779 active site 998088008780 homodimer interface [polypeptide binding]; other site 998088008781 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 998088008782 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 998088008783 inhibitor-cofactor binding pocket; inhibition site 998088008784 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008785 catalytic residue [active] 998088008786 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008787 NAD(P) binding site [chemical binding]; other site 998088008788 active site 998088008789 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 998088008790 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 998088008791 Protein export membrane protein; Region: SecD_SecF; cl14618 998088008792 Protein export membrane protein; Region: SecD_SecF; cl14618 998088008793 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 998088008794 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088008795 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088008796 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 998088008797 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088008798 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 998088008799 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 998088008800 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 998088008801 Predicted DNA-binding proteins [General function prediction only]; Region: COG1342 998088008802 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 998088008803 DNA binding residues [nucleotide binding] 998088008804 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 998088008805 GAF domain; Region: GAF; pfam01590 998088008806 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088008807 Zn2+ binding site [ion binding]; other site 998088008808 Mg2+ binding site [ion binding]; other site 998088008809 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 998088008810 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 998088008811 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 998088008812 FeS/SAM binding site; other site 998088008813 Protein of unknown function (DUF1349); Region: DUF1349; pfam07081 998088008814 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088008815 AAA domain; Region: AAA_23; pfam13476 998088008816 Walker A/P-loop; other site 998088008817 ATP binding site [chemical binding]; other site 998088008818 AAA domain; Region: AAA_21; pfam13304 998088008819 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 998088008820 threonine synthase; Validated; Region: PRK09225 998088008821 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088008822 catalytic residue [active] 998088008823 homoserine kinase; Provisional; Region: PRK01212 998088008824 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 998088008825 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 998088008826 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 998088008827 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 998088008828 putative catalytic residues [active] 998088008829 putative nucleotide binding site [chemical binding]; other site 998088008830 putative aspartate binding site [chemical binding]; other site 998088008831 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 998088008832 dimer interface [polypeptide binding]; other site 998088008833 putative threonine allosteric regulatory site; other site 998088008834 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 998088008835 putative threonine allosteric regulatory site; other site 998088008836 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 998088008837 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 998088008838 putative RNA methyltransferase; Provisional; Region: PRK10433 998088008839 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 998088008840 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 998088008841 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; pfam06315 998088008842 acyl-CoA thioesterase II; Provisional; Region: PRK10526 998088008843 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 998088008844 active site 998088008845 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 998088008846 catalytic triad [active] 998088008847 dimer interface [polypeptide binding]; other site 998088008848 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 998088008849 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 998088008850 RNA binding surface [nucleotide binding]; other site 998088008851 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 998088008852 probable active site [active] 998088008853 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 998088008854 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 998088008855 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 998088008856 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 998088008857 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 998088008858 active site 998088008859 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 998088008860 anthranilate synthase component I; Provisional; Region: PRK13564 998088008861 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 998088008862 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 998088008863 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 998088008864 Glutamine amidotransferase class-I; Region: GATase; pfam00117 998088008865 glutamine binding [chemical binding]; other site 998088008866 catalytic triad [active] 998088008867 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 998088008868 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 998088008869 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 998088008870 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 998088008871 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 998088008872 active site 998088008873 ribulose/triose binding site [chemical binding]; other site 998088008874 phosphate binding site [ion binding]; other site 998088008875 substrate (anthranilate) binding pocket [chemical binding]; other site 998088008876 product (indole) binding pocket [chemical binding]; other site 998088008877 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 998088008878 active site 998088008879 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 998088008880 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 998088008881 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008882 catalytic residue [active] 998088008883 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 998088008884 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 998088008885 substrate binding site [chemical binding]; other site 998088008886 active site 998088008887 catalytic residues [active] 998088008888 heterodimer interface [polypeptide binding]; other site 998088008889 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 998088008890 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cd03128 998088008891 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 998088008892 conserved cys residue [active] 998088008893 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 998088008894 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 998088008895 Nucleoside recognition; Region: Gate; pfam07670 998088008896 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 998088008897 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 998088008898 ArsC family; Region: ArsC; pfam03960 998088008899 catalytic residues [active] 998088008900 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 998088008901 Sodium Bile acid symporter family; Region: SBF; cl17470 998088008902 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 998088008903 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 998088008904 P loop; other site 998088008905 Nucleotide binding site [chemical binding]; other site 998088008906 DTAP/Switch II; other site 998088008907 Switch I; other site 998088008908 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 998088008909 P loop; other site 998088008910 Nucleotide binding site [chemical binding]; other site 998088008911 DTAP/Switch II; other site 998088008912 Switch I; other site 998088008913 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 998088008914 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 998088008915 dimerization interface [polypeptide binding]; other site 998088008916 putative DNA binding site [nucleotide binding]; other site 998088008917 putative Zn2+ binding site [ion binding]; other site 998088008918 META domain; Region: META; pfam03724 998088008919 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 998088008920 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 998088008921 two-component response regulator; Provisional; Region: PRK11173 998088008922 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 998088008923 active site 998088008924 phosphorylation site [posttranslational modification] 998088008925 intermolecular recognition site; other site 998088008926 dimerization interface [polypeptide binding]; other site 998088008927 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 998088008928 DNA binding site [nucleotide binding] 998088008929 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 998088008930 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 998088008931 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088008932 Walker A/P-loop; other site 998088008933 ATP binding site [chemical binding]; other site 998088008934 Q-loop/lid; other site 998088008935 ABC transporter signature motif; other site 998088008936 Walker B; other site 998088008937 D-loop; other site 998088008938 H-loop/switch region; other site 998088008939 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 998088008940 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088008941 Walker A/P-loop; other site 998088008942 ATP binding site [chemical binding]; other site 998088008943 Q-loop/lid; other site 998088008944 ABC transporter signature motif; other site 998088008945 Walker B; other site 998088008946 D-loop; other site 998088008947 H-loop/switch region; other site 998088008948 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 998088008949 Protein of unknown function, DUF488; Region: DUF488; cl01246 998088008950 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088008951 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 998088008952 NAD(P) binding site [chemical binding]; other site 998088008953 active site 998088008954 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 998088008955 homodimer interaction site [polypeptide binding]; other site 998088008956 cofactor binding site; other site 998088008957 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 998088008958 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 998088008959 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 998088008960 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 998088008961 active site 998088008962 phosphorylation site [posttranslational modification] 998088008963 intermolecular recognition site; other site 998088008964 dimerization interface [polypeptide binding]; other site 998088008965 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 998088008966 DNA binding site [nucleotide binding] 998088008967 sensor protein PhoQ; Provisional; Region: PRK10815 998088008968 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 998088008969 ATP binding site [chemical binding]; other site 998088008970 Mg2+ binding site [ion binding]; other site 998088008971 G-X-G motif; other site 998088008972 Uncharacterized conserved protein [Function unknown]; Region: COG1359 998088008973 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 998088008974 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088008975 Coenzyme A binding pocket [chemical binding]; other site 998088008976 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 998088008977 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 998088008978 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 998088008979 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 998088008980 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 998088008981 non-specific DNA binding site [nucleotide binding]; other site 998088008982 salt bridge; other site 998088008983 sequence-specific DNA binding site [nucleotide binding]; other site 998088008984 Cupin domain; Region: Cupin_2; pfam07883 998088008985 succinic semialdehyde dehydrogenase; Region: PLN02278 998088008986 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 998088008987 tetramerization interface [polypeptide binding]; other site 998088008988 NAD(P) binding site [chemical binding]; other site 998088008989 catalytic residues [active] 998088008990 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 998088008991 4-aminobutyrate aminotransferase; Provisional; Region: PRK07495 998088008992 inhibitor-cofactor binding pocket; inhibition site 998088008993 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088008994 catalytic residue [active] 998088008995 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 998088008996 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 998088008997 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 998088008998 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 998088008999 peptidyl-prolyl isomerase, gliding motility-associated; Region: ppisom_GldI; TIGR03516 998088009000 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 998088009001 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 998088009002 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 998088009003 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 998088009004 recombination associated protein; Reviewed; Region: rdgC; PRK00321 998088009005 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 998088009006 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088009007 Coenzyme A binding pocket [chemical binding]; other site 998088009008 exonuclease subunit SbcD; Provisional; Region: PRK10966 998088009009 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 998088009010 active site 998088009011 metal binding site [ion binding]; metal-binding site 998088009012 DNA binding site [nucleotide binding] 998088009013 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 998088009014 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088009015 AAA domain; Region: AAA_23; pfam13476 998088009016 Walker A/P-loop; other site 998088009017 ATP binding site [chemical binding]; other site 998088009018 Q-loop/lid; other site 998088009019 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088009020 Q-loop/lid; other site 998088009021 ABC transporter signature motif; other site 998088009022 Walker B; other site 998088009023 D-loop; other site 998088009024 H-loop/switch region; other site 998088009025 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 998088009026 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 998088009027 putative active site [active] 998088009028 metal binding site [ion binding]; metal-binding site 998088009029 pyruvate kinase; Provisional; Region: PRK09206 998088009030 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 998088009031 domain interfaces; other site 998088009032 active site 998088009033 hypothetical protein; Provisional; Region: PRK11281 998088009034 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 998088009035 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088009036 Integrase core domain; Region: rve_3; pfam13683 998088009037 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 998088009038 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 998088009039 active site 998088009040 Zn binding site [ion binding]; other site 998088009041 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 998088009042 putative active site [active] 998088009043 heme pocket [chemical binding]; other site 998088009044 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088009045 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088009046 metal binding site [ion binding]; metal-binding site 998088009047 active site 998088009048 I-site; other site 998088009049 PTS_IIA, PTS system, glucose/sucrose 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_glc; cd00210 998088009050 HPr interaction site; other site 998088009051 glycerol kinase (GK) interaction site [polypeptide binding]; other site 998088009052 active site 998088009053 phosphorylation site [posttranslational modification] 998088009054 phosphoenolpyruvate-protein phosphotransferase; Provisional; Region: PRK11177 998088009055 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 998088009056 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 998088009057 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 998088009058 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 998088009059 dimerization domain swap beta strand [polypeptide binding]; other site 998088009060 regulatory protein interface [polypeptide binding]; other site 998088009061 active site 998088009062 regulatory phosphorylation site [posttranslational modification]; other site 998088009063 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 998088009064 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 998088009065 dimer interface [polypeptide binding]; other site 998088009066 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088009067 catalytic residue [active] 998088009068 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 998088009069 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 998088009070 Walker A motif; other site 998088009071 ATP binding site [chemical binding]; other site 998088009072 Walker B motif; other site 998088009073 arginine finger; other site 998088009074 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 998088009075 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 998088009076 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 998088009077 dimer interface [polypeptide binding]; other site 998088009078 active site 998088009079 CoA binding pocket [chemical binding]; other site 998088009080 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 998088009081 dimerization interface [polypeptide binding]; other site 998088009082 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088009083 Zn2+ binding site [ion binding]; other site 998088009084 Mg2+ binding site [ion binding]; other site 998088009085 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 998088009086 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 998088009087 Walker A motif; other site 998088009088 ATP binding site [chemical binding]; other site 998088009089 Walker B motif; other site 998088009090 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 998088009091 type II secretion system protein C; Region: typeII_sec_gspC; TIGR01713 998088009092 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 998088009093 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 998088009094 type II secretion system protein D; Region: type_II_gspD; TIGR02517 998088009095 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 998088009096 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 998088009097 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 998088009098 type II secretion system protein E; Region: type_II_gspE; TIGR02533 998088009099 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 998088009100 Walker A motif; other site 998088009101 ATP binding site [chemical binding]; other site 998088009102 Walker B motif; other site 998088009103 type II secretion system protein F; Region: GspF; TIGR02120 998088009104 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 998088009105 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 998088009106 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 998088009107 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 998088009108 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 998088009109 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 998088009110 Type II transport protein GspH; Region: GspH; pfam12019 998088009111 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 998088009112 type II secretion system protein I; Region: gspI; TIGR01707 998088009113 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 998088009114 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 998088009115 type II secretion system protein J; Region: gspJ; TIGR01711 998088009116 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 998088009117 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 998088009118 Type II secretory pathway, component PulL [Intracellular trafficking and secretion]; Region: PulL; COG3297 998088009119 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 998088009120 GspL periplasmic domain; Region: GspL_C; pfam12693 998088009121 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 998088009122 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 998088009123 PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N; Region: PTS_IIB_chitobiose_lichenan; cd05564 998088009124 active site 998088009125 P-loop; other site 998088009126 phosphorylation site [posttranslational modification] 998088009127 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIC; Provisional; Region: PRK10297 998088009128 cellobiose phosphotransferase system IIC component; Reviewed; Region: celD; PRK09592 998088009129 Beta-glucosidase/6-phospho-beta-glucosidase/beta- galactosidase [Carbohydrate transport and metabolism]; Region: BglB; COG2723 998088009130 beta-galactosidase; Region: BGL; TIGR03356 998088009131 PTS_IIA, PTS system, lactose/cellobiose 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_lac; cd00215 998088009132 methionine cluster; other site 998088009133 active site 998088009134 phosphorylation site [posttranslational modification] 998088009135 metal binding site [ion binding]; metal-binding site 998088009136 DNA-binding transcriptional regulator ChbR; Provisional; Region: PRK10296 998088009137 Cupin domain; Region: Cupin_2; pfam07883 998088009138 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088009139 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 998088009140 Glycoside Hydrolases Family 4; Phospho-beta-glucosidase; Region: GH4_P_beta_glucosidase; cd05296 998088009141 NAD binding site [chemical binding]; other site 998088009142 sugar binding site [chemical binding]; other site 998088009143 divalent metal binding site [ion binding]; other site 998088009144 tetramer (dimer of dimers) interface [polypeptide binding]; other site 998088009145 dimer interface [polypeptide binding]; other site 998088009146 Enterococcus faecalis EF3048 and similar proteins; Region: YdjC_EF3048_like; cd10803 998088009147 putative active site [active] 998088009148 YdjC motif; other site 998088009149 Mg binding site [ion binding]; other site 998088009150 putative homodimer interface [polypeptide binding]; other site 998088009151 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 998088009152 YccA-like proteins; Region: YccA_like; cd10433 998088009153 TIGR01666 family membrane protein; Region: YCCS 998088009154 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 998088009155 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 998088009156 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 998088009157 sulfur relay protein, TusE/DsrC/DsvC family; Region: dsrC_tusE_dsvC; TIGR03342 998088009158 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 998088009159 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 998088009160 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088009161 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 998088009162 putative DNA binding site [nucleotide binding]; other site 998088009163 putative Zn2+ binding site [ion binding]; other site 998088009164 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 998088009165 substrate binding pocket [chemical binding]; other site 998088009166 dimerization interface [polypeptide binding]; other site 998088009167 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 998088009168 Lin1944 and related proteins, classical (c) SDRs; Region: Lin1944_like_SDR_c; cd11731 998088009169 putative NAD(P) binding site [chemical binding]; other site 998088009170 homodimer interface [polypeptide binding]; other site 998088009171 DinB family; Region: DinB; cl17821 998088009172 DinB superfamily; Region: DinB_2; pfam12867 998088009173 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 998088009174 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088009175 ligand binding site [chemical binding]; other site 998088009176 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 998088009177 Fic/DOC family; Region: Fic; pfam02661 998088009178 hypothetical protein; Provisional; Region: PRK01254 998088009179 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 998088009180 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 998088009181 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 998088009182 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 998088009183 Protein export membrane protein; Region: SecD_SecF; cl14618 998088009184 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 998088009185 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088009186 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088009187 Cache domain; Region: Cache_1; pfam02743 998088009188 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088009189 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088009190 metal binding site [ion binding]; metal-binding site 998088009191 active site 998088009192 I-site; other site 998088009193 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 998088009194 nucleophile elbow; other site 998088009195 L-type amino acid transporter; Region: 2A0308; TIGR00911 998088009196 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 998088009197 non-specific DNA binding site [nucleotide binding]; other site 998088009198 salt bridge; other site 998088009199 sequence-specific DNA binding site [nucleotide binding]; other site 998088009200 OmpA-like transmembrane domain; Region: OmpA_membrane; pfam01389 998088009201 outer membrane protein A; Reviewed; Region: PRK10808 998088009202 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088009203 ligand binding site [chemical binding]; other site 998088009204 outer membrane protein A; Reviewed; Region: PRK10808 998088009205 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 998088009206 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088009207 ligand binding site [chemical binding]; other site 998088009208 outer membrane protein A; Reviewed; Region: PRK10808 998088009209 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 998088009210 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088009211 ligand binding site [chemical binding]; other site 998088009212 malate dehydrogenase; Provisional; Region: PRK13529 998088009213 Malic enzyme, N-terminal domain; Region: malic; pfam00390 998088009214 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 998088009215 NAD(P) binding site [chemical binding]; other site 998088009216 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088009217 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088009218 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 998088009219 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 998088009220 hypothetical protein; Provisional; Region: PRK11037 998088009221 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088009222 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088009223 metal binding site [ion binding]; metal-binding site 998088009224 active site 998088009225 I-site; other site 998088009226 xanthine permease; Region: pbuX; TIGR03173 998088009227 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 998088009228 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 998088009229 Part of AAA domain; Region: AAA_19; pfam13245 998088009230 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 998088009231 AAA domain; Region: AAA_12; pfam13087 998088009232 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 998088009233 putative active site [active] 998088009234 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 998088009235 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 998088009236 amino acid carrier protein; Region: agcS; TIGR00835 998088009237 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 998088009238 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 998088009239 dimer interface [polypeptide binding]; other site 998088009240 active site 998088009241 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088009242 catalytic residues [active] 998088009243 substrate binding site [chemical binding]; other site 998088009244 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 998088009245 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 998088009246 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 998088009247 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 998088009248 catalytic triad [active] 998088009249 dimer interface [polypeptide binding]; other site 998088009250 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 998088009251 acyl-activating enzyme (AAE) consensus motif; other site 998088009252 active site 998088009253 AMP binding site [chemical binding]; other site 998088009254 CoA binding site [chemical binding]; other site 998088009255 isopentenyl-diphosphate delta-isomerase, type 1; Region: IPP_isom_1; TIGR02150 998088009256 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 998088009257 nudix motif; other site 998088009258 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 998088009259 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 998088009260 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 998088009261 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 998088009262 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 998088009263 Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]; Region: CutC; COG3142 998088009264 fructokinase; Reviewed; Region: PRK09557 998088009265 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 998088009266 nucleotide binding site [chemical binding]; other site 998088009267 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088009268 Coenzyme A binding pocket [chemical binding]; other site 998088009269 Peptidase family M48; Region: Peptidase_M48; pfam01435 998088009270 PBP superfamily domain; Region: PBP_like_2; cl17296 998088009271 phosphate regulon sensor protein; Provisional; Region: phoR; PRK11006 998088009272 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 998088009273 PAS domain; Region: PAS; smart00091 998088009274 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 998088009275 dimer interface [polypeptide binding]; other site 998088009276 phosphorylation site [posttranslational modification] 998088009277 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 998088009278 ATP binding site [chemical binding]; other site 998088009279 Mg2+ binding site [ion binding]; other site 998088009280 G-X-G motif; other site 998088009281 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 998088009282 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 998088009283 active site 998088009284 phosphorylation site [posttranslational modification] 998088009285 intermolecular recognition site; other site 998088009286 dimerization interface [polypeptide binding]; other site 998088009287 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 998088009288 DNA binding site [nucleotide binding] 998088009289 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 998088009290 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 998088009291 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 998088009292 GAF domain; Region: GAF; pfam01590 998088009293 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 998088009294 Walker A motif; other site 998088009295 ATP binding site [chemical binding]; other site 998088009296 Walker B motif; other site 998088009297 arginine finger; other site 998088009298 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 998088009299 DNA-binding interface [nucleotide binding]; DNA binding site 998088009300 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 998088009301 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 998088009302 NAD(P) binding site [chemical binding]; other site 998088009303 catalytic residues [active] 998088009304 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 998088009305 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088009306 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 998088009307 EamA-like transporter family; Region: EamA; pfam00892 998088009308 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 998088009309 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 998088009310 active site 998088009311 phosphorylation site [posttranslational modification] 998088009312 intermolecular recognition site; other site 998088009313 dimerization interface [polypeptide binding]; other site 998088009314 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 998088009315 PAS domain; Region: PAS; smart00091 998088009316 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 998088009317 ATP binding site [chemical binding]; other site 998088009318 Mg2+ binding site [ion binding]; other site 998088009319 G-X-G motif; other site 998088009320 malate dehydrogenase; Provisional; Region: PRK13529 998088009321 Malic enzyme, N-terminal domain; Region: malic; pfam00390 998088009322 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 998088009323 NAD(P) binding pocket [chemical binding]; other site 998088009324 2-hydroxycarboxylate transporter family; Region: 2HCT; pfam03390 998088009325 transcriptional regulator SlyA; Provisional; Region: PRK03573 998088009326 MarR family; Region: MarR; pfam01047 998088009327 multidrug resistance protein MdtN; Provisional; Region: PRK10476 998088009328 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088009329 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088009330 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 998088009331 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 998088009332 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088009333 substrate binding pocket [chemical binding]; other site 998088009334 membrane-bound complex binding site; other site 998088009335 hinge residues; other site 998088009336 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 998088009337 Gram-negative bacterial tonB protein; Region: TonB; cl10048 998088009338 Proteolipid membrane potential modulator; Region: Pmp3; pfam01679 998088009339 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 998088009340 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 998088009341 FeS/SAM binding site; other site 998088009342 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 998088009343 ATP cone domain; Region: ATP-cone; pfam03477 998088009344 Class III ribonucleotide reductase; Region: RNR_III; cd01675 998088009345 effector binding site; other site 998088009346 active site 998088009347 Zn binding site [ion binding]; other site 998088009348 glycine loop; other site 998088009349 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 998088009350 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 998088009351 nucleotide binding pocket [chemical binding]; other site 998088009352 K-X-D-G motif; other site 998088009353 catalytic site [active] 998088009354 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 998088009355 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 998088009356 Dimer interface [polypeptide binding]; other site 998088009357 BRCT sequence motif; other site 998088009358 Cell division protein [Cell division and chromosome partitioning]; Region: ZipA; COG3115 998088009359 ZipA, C-terminal FtsZ-binding domain; Region: ZipA_C; pfam04354 998088009360 FtsZ protein binding site [polypeptide binding]; other site 998088009361 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 998088009362 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 998088009363 Walker A/P-loop; other site 998088009364 ATP binding site [chemical binding]; other site 998088009365 Q-loop/lid; other site 998088009366 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 998088009367 ABC transporter signature motif; other site 998088009368 Walker B; other site 998088009369 D-loop; other site 998088009370 H-loop/switch region; other site 998088009371 putative sulfate transport protein CysZ; Validated; Region: PRK04949 998088009372 Predicted membrane protein [Function unknown]; Region: COG2860 998088009373 UPF0126 domain; Region: UPF0126; pfam03458 998088009374 UPF0126 domain; Region: UPF0126; pfam03458 998088009375 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 998088009376 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 998088009377 Peptidase M15; Region: Peptidase_M15_3; cl01194 998088009378 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 998088009379 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 998088009380 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088009381 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088009382 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 998088009383 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088009384 substrate binding pocket [chemical binding]; other site 998088009385 membrane-bound complex binding site; other site 998088009386 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 998088009387 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 998088009388 Ligand binding site; other site 998088009389 Putative Catalytic site; other site 998088009390 DXD motif; other site 998088009391 Predicted membrane protein [Function unknown]; Region: COG2246 998088009392 GtrA-like protein; Region: GtrA; pfam04138 998088009393 alpha-amylase; Reviewed; Region: malS; PRK09505 998088009394 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 998088009395 active site 998088009396 catalytic site [active] 998088009397 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 998088009398 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 998088009399 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 998088009400 putative N-terminal domain interface [polypeptide binding]; other site 998088009401 putative dimer interface [polypeptide binding]; other site 998088009402 putative substrate binding pocket (H-site) [chemical binding]; other site 998088009403 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 998088009404 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 998088009405 active site 998088009406 phosphorylation site [posttranslational modification] 998088009407 intermolecular recognition site; other site 998088009408 dimerization interface [polypeptide binding]; other site 998088009409 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 998088009410 DNA binding residues [nucleotide binding] 998088009411 dimerization interface [polypeptide binding]; other site 998088009412 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088009413 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088009414 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 998088009415 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 998088009416 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 998088009417 nucleophile elbow; other site 998088009418 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 998088009419 putative cation:proton antiport protein; Provisional; Region: PRK10669 998088009420 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 998088009421 TrkA-N domain; Region: TrkA_N; pfam02254 998088009422 TrkA-C domain; Region: TrkA_C; pfam02080 998088009423 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088009424 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088009425 metal binding site [ion binding]; metal-binding site 998088009426 active site 998088009427 I-site; other site 998088009428 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 998088009429 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 998088009430 Ligand Binding Site [chemical binding]; other site 998088009431 TilS substrate binding domain; Region: TilS; pfam09179 998088009432 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 998088009433 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 998088009434 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 998088009435 active site 998088009436 Zn binding site [ion binding]; other site 998088009437 Periplasmic lysozyme inhibitor, I-type (PliI) and similar proteins; Region: PliI_like; cd09632 998088009438 dimer interface [polypeptide binding]; other site 998088009439 putative inhibitory loop; other site 998088009440 pyridoxamine kinase; Validated; Region: PRK05756 998088009441 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 998088009442 dimer interface [polypeptide binding]; other site 998088009443 pyridoxal binding site [chemical binding]; other site 998088009444 ATP binding site [chemical binding]; other site 998088009445 lysine decarboxylase CadA; Provisional; Region: PRK15400 998088009446 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 998088009447 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 998088009448 homodimer interface [polypeptide binding]; other site 998088009449 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088009450 catalytic residue [active] 998088009451 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 998088009452 lysine/cadaverine antiporter; Provisional; Region: cadB; PRK10435 998088009453 DNA-binding transcriptional activator CadC; Provisional; Region: PRK10153 998088009454 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 998088009455 DNA binding site [nucleotide binding] 998088009456 putative transporter; Provisional; Region: PRK11021 998088009457 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088009458 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088009459 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 998088009460 putative effector binding pocket; other site 998088009461 dimerization interface [polypeptide binding]; other site 998088009462 putative hydrolase; Provisional; Region: PRK02113 998088009463 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 998088009464 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 998088009465 membrane-bound complex binding site; other site 998088009466 hinge residues; other site 998088009467 serine transporter; Region: stp; TIGR00814 998088009468 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088009469 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088009470 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088009471 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 998088009472 dimerization interface [polypeptide binding]; other site 998088009473 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 998088009474 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 998088009475 acetolactate synthase; Reviewed; Region: PRK08617 998088009476 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 998088009477 PYR/PP interface [polypeptide binding]; other site 998088009478 dimer interface [polypeptide binding]; other site 998088009479 TPP binding site [chemical binding]; other site 998088009480 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 998088009481 Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2...; Region: TPP_ALS; cd02010 998088009482 TPP-binding site [chemical binding]; other site 998088009483 dimer interface [polypeptide binding]; other site 998088009484 Alpha-acetolactate decarboxylase; Region: AAL_decarboxy; pfam03306 998088009485 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088009486 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088009487 The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; Region: PBP2_BudR; cd08451 998088009488 putative dimerization interface [polypeptide binding]; other site 998088009489 putative substrate binding pocket [chemical binding]; other site 998088009490 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 998088009491 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 998088009492 active site 998088009493 HIGH motif; other site 998088009494 dimer interface [polypeptide binding]; other site 998088009495 KMSKS motif; other site 998088009496 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 998088009497 RNA binding surface [nucleotide binding]; other site 998088009498 putative peptidase; Provisional; Region: PRK11649 998088009499 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 998088009500 Peptidase family M23; Region: Peptidase_M23; pfam01551 998088009501 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 998088009502 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 998088009503 homotrimer interaction site [polypeptide binding]; other site 998088009504 putative active site [active] 998088009505 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 998088009506 homotrimer interaction site [polypeptide binding]; other site 998088009507 putative active site [active] 998088009508 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 998088009509 homotrimer interaction site [polypeptide binding]; other site 998088009510 putative active site [active] 998088009511 transketolase; Reviewed; Region: PRK12753 998088009512 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 998088009513 TPP-binding site [chemical binding]; other site 998088009514 dimer interface [polypeptide binding]; other site 998088009515 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 998088009516 PYR/PP interface [polypeptide binding]; other site 998088009517 dimer interface [polypeptide binding]; other site 998088009518 TPP binding site [chemical binding]; other site 998088009519 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 998088009520 S-adenosylmethionine synthetase; Validated; Region: PRK05250 998088009521 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 998088009522 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 998088009523 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 998088009524 SprT homologues; Region: SprT; cl01182 998088009525 hypothetical protein; Provisional; Region: PRK04860 998088009526 Endonuclease I [DNA replication, recombination, and repair]; Region: EndA; COG2356 998088009527 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 998088009528 RNA methyltransferase, RsmE family; Region: TIGR00046 998088009529 glutathione synthetase; Provisional; Region: PRK05246 998088009530 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 998088009531 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 998088009532 hypothetical protein; Validated; Region: PRK00228 998088009533 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 998088009534 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 998088009535 POT family; Region: PTR2; cl17359 998088009536 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 998088009537 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088009538 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 998088009539 substrate binding pocket [chemical binding]; other site 998088009540 dimerization interface [polypeptide binding]; other site 998088009541 multidrug efflux system protein MdtL; Provisional; Region: PRK10473 998088009542 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 998088009543 putative substrate translocation pore; other site 998088009544 MoxR-like ATPases [General function prediction only]; Region: COG0714 998088009545 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 998088009546 Walker A motif; other site 998088009547 ATP binding site [chemical binding]; other site 998088009548 Walker B motif; other site 998088009549 arginine finger; other site 998088009550 Protein of unknown function DUF58; Region: DUF58; pfam01882 998088009551 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 998088009552 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 998088009553 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 998088009554 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 998088009555 amino acid carrier protein; Region: agcS; TIGR00835 998088009556 transaldolase-like protein; Provisional; Region: PTZ00411 998088009557 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 998088009558 active site 998088009559 dimer interface [polypeptide binding]; other site 998088009560 catalytic residue [active] 998088009561 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 998088009562 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 998088009563 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 998088009564 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 998088009565 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 998088009566 putative active site [active] 998088009567 putative PHP Thumb interface [polypeptide binding]; other site 998088009568 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 998088009569 generic binding surface II; other site 998088009570 generic binding surface I; other site 998088009571 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 998088009572 RNA/DNA hybrid binding site [nucleotide binding]; other site 998088009573 active site 998088009574 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 998088009575 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 998088009576 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 998088009577 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 998088009578 active site 998088009579 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 998088009580 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 998088009581 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 998088009582 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 998088009583 trimer interface [polypeptide binding]; other site 998088009584 active site 998088009585 UDP-GlcNAc binding site [chemical binding]; other site 998088009586 lipid binding site [chemical binding]; lipid-binding site 998088009587 periplasmic chaperone; Provisional; Region: PRK10780 998088009588 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 998088009589 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 998088009590 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 998088009591 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 998088009592 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 998088009593 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 998088009594 Surface antigen; Region: Bac_surface_Ag; pfam01103 998088009595 zinc metallopeptidase RseP; Provisional; Region: PRK10779 998088009596 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 998088009597 active site 998088009598 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 998088009599 protein binding site [polypeptide binding]; other site 998088009600 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 998088009601 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 998088009602 putative substrate binding region [chemical binding]; other site 998088009603 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 998088009604 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 998088009605 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 998088009606 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 998088009607 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 998088009608 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 998088009609 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 998088009610 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 998088009611 catalytic residue [active] 998088009612 putative FPP diphosphate binding site; other site 998088009613 putative FPP binding hydrophobic cleft; other site 998088009614 dimer interface [polypeptide binding]; other site 998088009615 putative IPP diphosphate binding site; other site 998088009616 ribosome recycling factor; Reviewed; Region: frr; PRK00083 998088009617 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 998088009618 hinge region; other site 998088009619 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 998088009620 putative nucleotide binding site [chemical binding]; other site 998088009621 uridine monophosphate binding site [chemical binding]; other site 998088009622 homohexameric interface [polypeptide binding]; other site 998088009623 elongation factor Ts; Provisional; Region: tsf; PRK09377 998088009624 UBA/TS-N domain; Region: UBA; pfam00627 998088009625 Elongation factor TS; Region: EF_TS; pfam00889 998088009626 Elongation factor TS; Region: EF_TS; pfam00889 998088009627 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 998088009628 rRNA interaction site [nucleotide binding]; other site 998088009629 S8 interaction site; other site 998088009630 putative laminin-1 binding site; other site 998088009631 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 998088009632 active site 998088009633 PII uridylyl-transferase; Provisional; Region: PRK05007 998088009634 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 998088009635 metal binding triad; other site 998088009636 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 998088009637 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088009638 Zn2+ binding site [ion binding]; other site 998088009639 Mg2+ binding site [ion binding]; other site 998088009640 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 998088009641 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 998088009642 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 998088009643 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 998088009644 trimer interface [polypeptide binding]; other site 998088009645 active site 998088009646 substrate binding site [chemical binding]; other site 998088009647 CoA binding site [chemical binding]; other site 998088009648 hypothetical protein; Provisional; Region: PRK13677 998088009649 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 998088009650 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 998088009651 PTS_IIB, PTS system, glucose/sucrose specific IIB 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_IIB_glc; cd00212 998088009652 active site turn [active] 998088009653 phosphorylation site [posttranslational modification] 998088009654 Maltose operon periplasmic protein precursor (MalM); Region: MalM; pfam07148 998088009655 The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel...; Region: Maltoporin-like; cd01346 998088009656 trimer interface; other site 998088009657 sugar binding site [chemical binding]; other site 998088009658 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 998088009659 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 998088009660 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 998088009661 probable active site [active] 998088009662 tRNA pseudouridine synthase C; Region: DUF446; pfam04287 998088009663 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 998088009664 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 998088009665 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 998088009666 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; pfam10071 998088009667 Syd protein (SUKH-2); Region: Syd; pfam07348 998088009668 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 998088009669 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 998088009670 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 998088009671 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088009672 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088009673 metal binding site [ion binding]; metal-binding site 998088009674 active site 998088009675 I-site; other site 998088009676 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 998088009677 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 998088009678 flap endonuclease-like protein; Provisional; Region: PRK09482 998088009679 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 998088009680 active site 998088009681 metal binding site 1 [ion binding]; metal-binding site 998088009682 putative 5' ssDNA interaction site; other site 998088009683 metal binding site 3; metal-binding site 998088009684 metal binding site 2 [ion binding]; metal-binding site 998088009685 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 998088009686 putative DNA binding site [nucleotide binding]; other site 998088009687 putative metal binding site [ion binding]; other site 998088009688 tartrate dehydrogenase; Region: TTC; TIGR02089 998088009689 isocitrate dehydrogenase; Provisional; Region: PRK08997 998088009690 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 998088009691 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 998088009692 Protein of unknown function (DUF423); Region: DUF423; pfam04241 998088009693 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 998088009694 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 998088009695 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088009696 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 998088009697 dimerization interface [polypeptide binding]; other site 998088009698 substrate binding pocket [chemical binding]; other site 998088009699 Cache domain; Region: Cache_1; pfam02743 998088009700 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088009701 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 998088009702 dimerization interface [polypeptide binding]; other site 998088009703 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088009704 dimer interface [polypeptide binding]; other site 998088009705 putative CheW interface [polypeptide binding]; other site 998088009706 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 998088009707 active site 998088009708 DNA polymerase IV; Validated; Region: PRK02406 998088009709 DNA binding site [nucleotide binding] 998088009710 DJ-1 family protein; Region: not_thiJ; TIGR01383 998088009711 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 998088009712 conserved cys residue [active] 998088009713 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 998088009714 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 998088009715 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 998088009716 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 998088009717 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 998088009718 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; pfam03502 998088009719 muropeptide transporter; Reviewed; Region: ampG; PRK11902 998088009720 AmpG-like permease; Region: 2A0125; TIGR00901 998088009721 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 998088009722 active site 998088009723 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 998088009724 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 998088009725 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 998088009726 S-adenosylmethionine binding site [chemical binding]; other site 998088009727 BolA-like protein; Region: BolA; cl00386 998088009728 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 998088009729 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 998088009730 E3 interaction surface; other site 998088009731 lipoyl attachment site [posttranslational modification]; other site 998088009732 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 998088009733 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 998088009734 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 998088009735 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 998088009736 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 998088009737 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 998088009738 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 998088009739 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 998088009740 catalytic loop [active] 998088009741 iron binding site [ion binding]; other site 998088009742 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 998088009743 FAD binding pocket [chemical binding]; other site 998088009744 FAD binding motif [chemical binding]; other site 998088009745 phosphate binding motif [ion binding]; other site 998088009746 beta-alpha-beta structure motif; other site 998088009747 NAD binding pocket [chemical binding]; other site 998088009748 thiamine biosynthesis lipoprotein ApbE; Provisional; Region: PRK10461 998088009749 ApbE family; Region: ApbE; pfam02424 998088009750 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2991 998088009751 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 998088009752 Tryptophan-rich protein (DUF2389); Region: DUF2389; cl09726 998088009753 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 998088009754 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 998088009755 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 998088009756 S-adenosylmethionine binding site [chemical binding]; other site 998088009757 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 998088009758 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 998088009759 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 998088009760 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088009761 NAD(P) binding site [chemical binding]; other site 998088009762 active site 998088009763 SnoaL-like domain; Region: SnoaL_2; pfam12680 998088009764 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 998088009765 DNA photolyase; Region: DNA_photolyase; pfam00875 998088009766 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 998088009767 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 998088009768 DNA binding residues [nucleotide binding] 998088009769 Protein of unknown function (DUF523); Region: DUF523; pfam04463 998088009770 Uncharacterized conserved protein [Function unknown]; Region: COG3272 998088009771 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 998088009772 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 998088009773 TIGR00268 family protein; Region: TIGR00268 998088009774 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 998088009775 Ligand Binding Site [chemical binding]; other site 998088009776 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 998088009777 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 998088009778 motif II; other site 998088009779 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 998088009780 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 998088009781 Prephenate dehydratase; Region: PDT; pfam00800 998088009782 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 998088009783 putative L-Phe binding site [chemical binding]; other site 998088009784 LPP20 lipoprotein; Region: LPP20; pfam02169 998088009785 Predicted integral membrane protein [Function unknown]; Region: COG5616 998088009786 phage/plasmid-like protein TIGR03299; Region: LGT_TIGR03299 998088009787 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 998088009788 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 998088009789 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 998088009790 non-specific DNA binding site [nucleotide binding]; other site 998088009791 salt bridge; other site 998088009792 sequence-specific DNA binding site [nucleotide binding]; other site 998088009793 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 998088009794 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 998088009795 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 998088009796 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 998088009797 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 998088009798 Queuine tRNA-ribosyltransferase; Region: TGT; pfam01702 998088009799 DNA phosphorothioation-associated DGQHR protein 1; Region: DGQHR_dnd_1; TIGR04172 998088009800 DGQHR domain; Region: DGQHR; TIGR03187 998088009801 CRISPR-associated helicase Cas3, subtype CYANO; Region: cas3_cyano; TIGR03158 998088009802 DEAD/DEAH box helicase; Region: DEAD; pfam00270 998088009803 ATP binding site [chemical binding]; other site 998088009804 putative Mg++ binding site [ion binding]; other site 998088009805 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 998088009806 ATP-binding site [chemical binding]; other site 998088009807 DEAD-like helicases superfamily; Region: DEXDc; smart00487 998088009808 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 998088009809 ATP binding site [chemical binding]; other site 998088009810 putative Mg++ binding site [ion binding]; other site 998088009811 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 998088009812 nucleotide binding region [chemical binding]; other site 998088009813 ATP-binding site [chemical binding]; other site 998088009814 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 998088009815 ATP binding site [chemical binding]; other site 998088009816 putative Mg++ binding site [ion binding]; other site 998088009817 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 998088009818 nucleotide binding region [chemical binding]; other site 998088009819 ATP-binding site [chemical binding]; other site 998088009820 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 998088009821 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 998088009822 Catalytic site [active] 998088009823 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 998088009824 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 998088009825 active site 998088009826 DNA binding site [nucleotide binding] 998088009827 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 998088009828 Fic family protein [Function unknown]; Region: COG3177 998088009829 Fic/DOC family; Region: Fic; pfam02661 998088009830 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 998088009831 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 998088009832 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 998088009833 integrase; Provisional; Region: PRK09692 998088009834 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 998088009835 active site 998088009836 Int/Topo IB signature motif; other site 998088009837 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088009838 dimer interface [polypeptide binding]; other site 998088009839 putative CheW interface [polypeptide binding]; other site 998088009840 outer membrane porin, OprD family; Region: OprD; pfam03573 998088009841 short chain dehydrogenase; Provisional; Region: PRK05993 998088009842 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 998088009843 NADP binding site [chemical binding]; other site 998088009844 active site 998088009845 steroid binding site; other site 998088009846 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 998088009847 TraB family; Region: TraB; pfam01963 998088009848 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 998088009849 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 998088009850 Smr domain; Region: Smr; pfam01713 998088009851 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 998088009852 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 998088009853 active site 998088009854 Zn binding site [ion binding]; other site 998088009855 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; cd06587 998088009856 active site 998088009857 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 998088009858 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 998088009859 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 998088009860 Type II transport protein GspH; Region: GspH; pfam12019 998088009861 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 998088009862 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 998088009863 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 998088009864 AlkA N-terminal domain; Region: AlkA_N; pfam06029 998088009865 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 998088009866 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 998088009867 minor groove reading motif; other site 998088009868 helix-hairpin-helix signature motif; other site 998088009869 substrate binding pocket [chemical binding]; other site 998088009870 active site 998088009871 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 998088009872 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 998088009873 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 998088009874 DNA binding site [nucleotide binding] 998088009875 active site 998088009876 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 998088009877 Peptidase family U32; Region: Peptidase_U32; pfam01136 998088009878 Collagenase; Region: DUF3656; pfam12392 998088009879 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 998088009880 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088009881 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088009882 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 998088009883 substrate binding pocket [chemical binding]; other site 998088009884 dimerization interface [polypeptide binding]; other site 998088009885 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 998088009886 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 998088009887 dimer interface [polypeptide binding]; other site 998088009888 active site 998088009889 CoA binding pocket [chemical binding]; other site 998088009890 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088009891 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 998088009892 active site 998088009893 phosphorylation site [posttranslational modification] 998088009894 intermolecular recognition site; other site 998088009895 dimerization interface [polypeptide binding]; other site 998088009896 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 998088009897 anti sigma factor interaction site; other site 998088009898 regulatory phosphorylation site [posttranslational modification]; other site 998088009899 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 998088009900 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 998088009901 putative binding surface; other site 998088009902 active site 998088009903 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 998088009904 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 998088009905 ATP binding site [chemical binding]; other site 998088009906 Mg2+ binding site [ion binding]; other site 998088009907 G-X-G motif; other site 998088009908 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 998088009909 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088009910 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 998088009911 dimerization interface [polypeptide binding]; other site 998088009912 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088009913 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088009914 dimer interface [polypeptide binding]; other site 998088009915 putative CheW interface [polypeptide binding]; other site 998088009916 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 998088009917 putative CheA interaction surface; other site 998088009918 PAS domain; Region: PAS_9; pfam13426 998088009919 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088009920 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088009921 dimer interface [polypeptide binding]; other site 998088009922 putative CheW interface [polypeptide binding]; other site 998088009923 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 998088009924 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 998088009925 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 998088009926 S-adenosylmethionine binding site [chemical binding]; other site 998088009927 CheD chemotactic sensory transduction; Region: CheD; cl00810 998088009928 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 998088009929 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 998088009930 active site 998088009931 phosphorylation site [posttranslational modification] 998088009932 intermolecular recognition site; other site 998088009933 dimerization interface [polypeptide binding]; other site 998088009934 CheB methylesterase; Region: CheB_methylest; pfam01339 998088009935 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 998088009936 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 998088009937 RNase E interface [polypeptide binding]; other site 998088009938 trimer interface [polypeptide binding]; other site 998088009939 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 998088009940 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 998088009941 RNase E interface [polypeptide binding]; other site 998088009942 trimer interface [polypeptide binding]; other site 998088009943 active site 998088009944 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 998088009945 putative nucleic acid binding region [nucleotide binding]; other site 998088009946 G-X-X-G motif; other site 998088009947 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 998088009948 RNA binding site [nucleotide binding]; other site 998088009949 domain interface; other site 998088009950 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 998088009951 16S/18S rRNA binding site [nucleotide binding]; other site 998088009952 S13e-L30e interaction site [polypeptide binding]; other site 998088009953 25S rRNA binding site [nucleotide binding]; other site 998088009954 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 998088009955 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 998088009956 RNA binding site [nucleotide binding]; other site 998088009957 active site 998088009958 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 998088009959 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 998088009960 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 998088009961 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 998088009962 translation initiation factor IF-2; Region: IF-2; TIGR00487 998088009963 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 998088009964 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 998088009965 G1 box; other site 998088009966 putative GEF interaction site [polypeptide binding]; other site 998088009967 GTP/Mg2+ binding site [chemical binding]; other site 998088009968 Switch I region; other site 998088009969 G2 box; other site 998088009970 G3 box; other site 998088009971 Switch II region; other site 998088009972 G4 box; other site 998088009973 G5 box; other site 998088009974 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 998088009975 Translation-initiation factor 2; Region: IF-2; pfam11987 998088009976 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 998088009977 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 998088009978 NusA N-terminal domain; Region: NusA_N; pfam08529 998088009979 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 998088009980 RNA binding site [nucleotide binding]; other site 998088009981 homodimer interface [polypeptide binding]; other site 998088009982 NusA-like KH domain; Region: KH_5; pfam13184 998088009983 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 998088009984 G-X-X-G motif; other site 998088009985 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 998088009986 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 998088009987 Sm and related proteins; Region: Sm_like; cl00259 998088009988 ribosome maturation protein RimP; Reviewed; Region: PRK00092 998088009989 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 998088009990 putative oligomer interface [polypeptide binding]; other site 998088009991 putative RNA binding site [nucleotide binding]; other site 998088009992 Preprotein translocase SecG subunit; Region: SecG; pfam03840 998088009993 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 998088009994 substrate binding site [chemical binding]; other site 998088009995 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 998088009996 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 998088009997 active site 998088009998 substrate binding site [chemical binding]; other site 998088009999 metal binding site [ion binding]; metal-binding site 998088010000 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 998088010001 dihydropteroate synthase; Region: DHPS; TIGR01496 998088010002 substrate binding pocket [chemical binding]; other site 998088010003 dimer interface [polypeptide binding]; other site 998088010004 inhibitor binding site; inhibition site 998088010005 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 998088010006 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 998088010007 Walker A motif; other site 998088010008 ATP binding site [chemical binding]; other site 998088010009 Walker B motif; other site 998088010010 arginine finger; other site 998088010011 Peptidase family M41; Region: Peptidase_M41; pfam01434 998088010012 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 998088010013 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 998088010014 S-adenosylmethionine binding site [chemical binding]; other site 998088010015 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 998088010016 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 998088010017 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 998088010018 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 998088010019 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 998088010020 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 998088010021 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088010022 ligand binding site [chemical binding]; other site 998088010023 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 998088010024 flagellar motor protein MotP; Reviewed; Region: PRK06743 998088010025 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 998088010026 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 998088010027 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 998088010028 substrate binding pocket [chemical binding]; other site 998088010029 chain length determination region; other site 998088010030 substrate-Mg2+ binding site; other site 998088010031 catalytic residues [active] 998088010032 aspartate-rich region 1; other site 998088010033 active site lid residues [active] 998088010034 aspartate-rich region 2; other site 998088010035 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 998088010036 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 998088010037 TPP-binding site; other site 998088010038 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 998088010039 PYR/PP interface [polypeptide binding]; other site 998088010040 dimer interface [polypeptide binding]; other site 998088010041 TPP binding site [chemical binding]; other site 998088010042 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 998088010043 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 998088010044 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 998088010045 active site 998088010046 metal binding site [ion binding]; metal-binding site 998088010047 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 998088010048 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 998088010049 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 998088010050 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 998088010051 active site 998088010052 phosphorylation site [posttranslational modification] 998088010053 intermolecular recognition site; other site 998088010054 dimerization interface [polypeptide binding]; other site 998088010055 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 998088010056 Walker A motif; other site 998088010057 ATP binding site [chemical binding]; other site 998088010058 Walker B motif; other site 998088010059 arginine finger; other site 998088010060 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 998088010061 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 998088010062 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 998088010063 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 998088010064 FOG: WD40 repeat [General function prediction only]; Region: COG2319 998088010065 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 998088010066 structural tetrad; other site 998088010067 SlyX; Region: SlyX; pfam04102 998088010068 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 998088010069 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 998088010070 dimer interface [polypeptide binding]; other site 998088010071 conserved gate region; other site 998088010072 putative PBP binding loops; other site 998088010073 ABC-ATPase subunit interface; other site 998088010074 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 998088010075 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 998088010076 dimer interface [polypeptide binding]; other site 998088010077 conserved gate region; other site 998088010078 putative PBP binding loops; other site 998088010079 ABC-ATPase subunit interface; other site 998088010080 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 998088010081 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 998088010082 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 998088010083 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088010084 Walker A/P-loop; other site 998088010085 ATP binding site [chemical binding]; other site 998088010086 Q-loop/lid; other site 998088010087 ABC transporter signature motif; other site 998088010088 Walker B; other site 998088010089 D-loop; other site 998088010090 H-loop/switch region; other site 998088010091 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088010092 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088010093 Walker A/P-loop; other site 998088010094 ATP binding site [chemical binding]; other site 998088010095 Q-loop/lid; other site 998088010096 ABC transporter signature motif; other site 998088010097 Walker B; other site 998088010098 D-loop; other site 998088010099 H-loop/switch region; other site 998088010100 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 998088010101 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 998088010102 tetramer interfaces [polypeptide binding]; other site 998088010103 binuclear metal-binding site [ion binding]; other site 998088010104 thiamine monophosphate kinase; Provisional; Region: PRK05731 998088010105 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 998088010106 ATP binding site [chemical binding]; other site 998088010107 dimerization interface [polypeptide binding]; other site 998088010108 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 998088010109 putative RNA binding site [nucleotide binding]; other site 998088010110 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 998088010111 homopentamer interface [polypeptide binding]; other site 998088010112 active site 998088010113 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 998088010114 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 998088010115 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 998088010116 dimerization interface [polypeptide binding]; other site 998088010117 active site 998088010118 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 998088010119 Lumazine binding domain; Region: Lum_binding; pfam00677 998088010120 Lumazine binding domain; Region: Lum_binding; pfam00677 998088010121 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 998088010122 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 998088010123 catalytic motif [active] 998088010124 Zn binding site [ion binding]; other site 998088010125 RibD C-terminal domain; Region: RibD_C; cl17279 998088010126 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 998088010127 ATP cone domain; Region: ATP-cone; pfam03477 998088010128 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 998088010129 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 998088010130 dimer interface [polypeptide binding]; other site 998088010131 active site 998088010132 glycine-pyridoxal phosphate binding site [chemical binding]; other site 998088010133 folate binding site [chemical binding]; other site 998088010134 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 998088010135 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 998088010136 dimerization interface [polypeptide binding]; other site 998088010137 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 998088010138 dimer interface [polypeptide binding]; other site 998088010139 phosphorylation site [posttranslational modification] 998088010140 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 998088010141 ATP binding site [chemical binding]; other site 998088010142 Mg2+ binding site [ion binding]; other site 998088010143 G-X-G motif; other site 998088010144 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 998088010145 active site 998088010146 phosphorylation site [posttranslational modification] 998088010147 intermolecular recognition site; other site 998088010148 dimerization interface [polypeptide binding]; other site 998088010149 TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria; Region: PBP1_TorT-like; cd06306 998088010150 TMAO reductase system periplasmic protein TorT; Region: TMAO_TorT; TIGR02955 998088010151 putative ligand binding site [chemical binding]; other site 998088010152 Uncharacterized conserved protein [Function unknown]; Region: COG3791 998088010153 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 998088010154 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 998088010155 active site 998088010156 phosphorylation site [posttranslational modification] 998088010157 intermolecular recognition site; other site 998088010158 dimerization interface [polypeptide binding]; other site 998088010159 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 998088010160 DNA binding site [nucleotide binding] 998088010161 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 998088010162 trimethylamine N-oxide reductase cytochrome c-type subunit; Provisional; Region: PRK15032 998088010163 trimethylamine N-oxide reductase I catalytic subunit; Provisional; Region: PRK15102 998088010164 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 998088010165 molybdopterin cofactor binding site [chemical binding]; other site 998088010166 substrate binding site [chemical binding]; other site 998088010167 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 998088010168 molybdopterin cofactor binding site; other site 998088010169 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 998088010170 PAS fold; Region: PAS_4; pfam08448 998088010171 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 998088010172 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 998088010173 PAS domain; Region: PAS_9; pfam13426 998088010174 putative active site [active] 998088010175 heme pocket [chemical binding]; other site 998088010176 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088010177 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088010178 metal binding site [ion binding]; metal-binding site 998088010179 active site 998088010180 I-site; other site 998088010181 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 998088010182 acetyl-CoA synthetase; Provisional; Region: PRK00174 998088010183 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 998088010184 active site 998088010185 CoA binding site [chemical binding]; other site 998088010186 acyl-activating enzyme (AAE) consensus motif; other site 998088010187 AMP binding site [chemical binding]; other site 998088010188 acetate binding site [chemical binding]; other site 998088010189 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 998088010190 Dehydroquinase class II; Region: DHquinase_II; pfam01220 998088010191 active site 998088010192 trimer interface [polypeptide binding]; other site 998088010193 dimer interface [polypeptide binding]; other site 998088010194 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 998088010195 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 998088010196 carboxyltransferase (CT) interaction site; other site 998088010197 biotinylation site [posttranslational modification]; other site 998088010198 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 998088010199 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 998088010200 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 998088010201 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 998088010202 Protein of unknown function (DUF997); Region: DUF997; cl01614 998088010203 Na(+)/pantothenate cotransporters: PanF of Escherichia coli and related proteins; solute binding domain; Region: SLC5sbd_PanF; cd10327 998088010204 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 998088010205 Na binding site [ion binding]; other site 998088010206 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 998088010207 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 998088010208 PTS_IIB, PTS system, glucose/sucrose specific IIB 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_IIB_glc; cl00164 998088010209 active site turn [active] 998088010210 phosphorylation site [posttranslational modification] 998088010211 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088010212 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088010213 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 998088010214 putative effector binding pocket; other site 998088010215 dimerization interface [polypeptide binding]; other site 998088010216 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 998088010217 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 998088010218 putative NAD(P) binding site [chemical binding]; other site 998088010219 dimer interface [polypeptide binding]; other site 998088010220 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 998088010221 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 998088010222 S-adenosylmethionine binding site [chemical binding]; other site 998088010223 Putative D-3-Phosphoglycerate Dehydrogenases; Region: PGDH_like_1; cd12169 998088010224 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 998088010225 dimerization interface [polypeptide binding]; other site 998088010226 NAD binding site [chemical binding]; other site 998088010227 ligand binding site [chemical binding]; other site 998088010228 catalytic site [active] 998088010229 maltose O-acetyltransferase; Provisional; Region: PRK10092 998088010230 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 998088010231 active site 998088010232 substrate binding site [chemical binding]; other site 998088010233 trimer interface [polypeptide binding]; other site 998088010234 CoA binding site [chemical binding]; other site 998088010235 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 998088010236 putative FMN binding site [chemical binding]; other site 998088010237 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 998088010238 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 998088010239 active site 998088010240 FMN binding site [chemical binding]; other site 998088010241 2,4-decadienoyl-CoA binding site; other site 998088010242 catalytic residue [active] 998088010243 4Fe-4S cluster binding site [ion binding]; other site 998088010244 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 998088010245 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 998088010246 protease 4; Provisional; Region: PRK10949 998088010247 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 998088010248 tandem repeat interface [polypeptide binding]; other site 998088010249 oligomer interface [polypeptide binding]; other site 998088010250 active site residues [active] 998088010251 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 998088010252 tandem repeat interface [polypeptide binding]; other site 998088010253 oligomer interface [polypeptide binding]; other site 998088010254 active site residues [active] 998088010255 L,D-transpeptidase; Provisional; Region: PRK10190 998088010256 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088010257 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088010258 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 998088010259 binding surface 998088010260 TPR motif; other site 998088010261 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 998088010262 binding surface 998088010263 TPR motif; other site 998088010264 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 998088010265 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 998088010266 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 998088010267 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 998088010268 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 998088010269 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 998088010270 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 998088010271 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 998088010272 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 998088010273 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 998088010274 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 998088010275 dimer interface [polypeptide binding]; other site 998088010276 conserved gate region; other site 998088010277 putative PBP binding loops; other site 998088010278 ABC-ATPase subunit interface; other site 998088010279 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 998088010280 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 998088010281 dimer interface [polypeptide binding]; other site 998088010282 conserved gate region; other site 998088010283 putative PBP binding loops; other site 998088010284 ABC-ATPase subunit interface; other site 998088010285 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 998088010286 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 998088010287 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 998088010288 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088010289 Walker A/P-loop; other site 998088010290 ATP binding site [chemical binding]; other site 998088010291 Q-loop/lid; other site 998088010292 ABC transporter signature motif; other site 998088010293 Walker B; other site 998088010294 D-loop; other site 998088010295 H-loop/switch region; other site 998088010296 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 998088010297 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 998088010298 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 998088010299 Walker A/P-loop; other site 998088010300 ATP binding site [chemical binding]; other site 998088010301 Q-loop/lid; other site 998088010302 ABC transporter signature motif; other site 998088010303 Walker B; other site 998088010304 D-loop; other site 998088010305 H-loop/switch region; other site 998088010306 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 998088010307 Uncharacterized conserved protein [Function unknown]; Region: COG1284 998088010308 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 998088010309 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 998088010310 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 998088010311 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 998088010312 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 998088010313 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 998088010314 putative NAD(P) binding site [chemical binding]; other site 998088010315 active site 998088010316 putative substrate binding site [chemical binding]; other site 998088010317 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; pfam09849 998088010318 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; pfam09849 998088010319 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 998088010320 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 998088010321 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 998088010322 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088010323 catalytic residue [active] 998088010324 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 998088010325 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 998088010326 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 998088010327 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088010328 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088010329 ABC transporter; Region: ABC_tran_2; pfam12848 998088010330 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 998088010331 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 998088010332 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 998088010333 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 998088010334 HIGH motif; other site 998088010335 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 998088010336 active site 998088010337 KMSKS motif; other site 998088010338 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 998088010339 dimerization interface [polypeptide binding]; other site 998088010340 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088010341 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088010342 dimer interface [polypeptide binding]; other site 998088010343 putative CheW interface [polypeptide binding]; other site 998088010344 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 998088010345 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 998088010346 DNA-binding site [nucleotide binding]; DNA binding site 998088010347 RNA-binding motif; other site 998088010348 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 998088010349 putative active site [active] 998088010350 putative substrate binding site [chemical binding]; other site 998088010351 catalytic site [active] 998088010352 dimer interface [polypeptide binding]; other site 998088010353 GTPase RsgA; Reviewed; Region: PRK12288 998088010354 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 998088010355 RNA binding site [nucleotide binding]; other site 998088010356 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 998088010357 GTPase/Zn-binding domain interface [polypeptide binding]; other site 998088010358 GTP/Mg2+ binding site [chemical binding]; other site 998088010359 G4 box; other site 998088010360 G5 box; other site 998088010361 G1 box; other site 998088010362 Switch I region; other site 998088010363 G2 box; other site 998088010364 G3 box; other site 998088010365 Switch II region; other site 998088010366 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 998088010367 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 998088010368 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 998088010369 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 998088010370 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 998088010371 putative catalytic cysteine [active] 998088010372 gamma-glutamyl kinase; Provisional; Region: PRK05429 998088010373 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 998088010374 homotetrameric interface [polypeptide binding]; other site 998088010375 putative phosphate binding site [ion binding]; other site 998088010376 putative allosteric binding site; other site 998088010377 nucleotide binding site [chemical binding]; other site 998088010378 PUA domain; Region: PUA; pfam01472 998088010379 DNA-binding transcriptional regulator Crl; Provisional; Region: PRK10984 998088010380 fermentation/respiration switch protein; Reviewed; Region: frsA; PRK05077 998088010381 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 998088010382 active site 998088010383 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 998088010384 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 998088010385 metal binding site [ion binding]; metal-binding site 998088010386 dimer interface [polypeptide binding]; other site 998088010387 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 998088010388 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 998088010389 putative metal binding site [ion binding]; other site 998088010390 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 998088010391 HSP70 interaction site [polypeptide binding]; other site 998088010392 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 998088010393 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 998088010394 Substrate binding site; other site 998088010395 metal-binding site 998088010396 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 998088010397 Phosphotransferase enzyme family; Region: APH; pfam01636 998088010398 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 998088010399 OstA-like protein; Region: OstA; cl00844 998088010400 Organic solvent tolerance protein; Region: OstA_C; pfam04453 998088010401 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 998088010402 SurA N-terminal domain; Region: SurA_N; pfam09312 998088010403 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 998088010404 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 998088010405 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 998088010406 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 998088010407 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 998088010408 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 998088010409 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 998088010410 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 998088010411 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 998088010412 active site 998088010413 metal binding site [ion binding]; metal-binding site 998088010414 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 998088010415 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 998088010416 non-specific DNA binding site [nucleotide binding]; other site 998088010417 salt bridge; other site 998088010418 sequence-specific DNA binding site [nucleotide binding]; other site 998088010419 2TM domain; Region: 2TM; pfam13239 998088010420 hypothetical protein; Provisional; Region: PRK10508 998088010421 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 998088010422 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 998088010423 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 998088010424 Nucleoside recognition; Region: Gate; pfam07670 998088010425 GTPase CgtA; Reviewed; Region: obgE; PRK12298 998088010426 GTP1/OBG; Region: GTP1_OBG; pfam01018 998088010427 Obg GTPase; Region: Obg; cd01898 998088010428 G1 box; other site 998088010429 GTP/Mg2+ binding site [chemical binding]; other site 998088010430 Switch I region; other site 998088010431 G2 box; other site 998088010432 G3 box; other site 998088010433 Switch II region; other site 998088010434 G4 box; other site 998088010435 G5 box; other site 998088010436 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 998088010437 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 998088010438 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 998088010439 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 998088010440 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 998088010441 substrate binding pocket [chemical binding]; other site 998088010442 chain length determination region; other site 998088010443 substrate-Mg2+ binding site; other site 998088010444 catalytic residues [active] 998088010445 aspartate-rich region 1; other site 998088010446 active site lid residues [active] 998088010447 aspartate-rich region 2; other site 998088010448 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 998088010449 FtsH protease regulator HflC; Provisional; Region: PRK11029 998088010450 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 998088010451 FtsH protease regulator HflK; Provisional; Region: PRK10930 998088010452 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 998088010453 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 998088010454 GTPase HflX; Provisional; Region: PRK11058 998088010455 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 998088010456 HflX GTPase family; Region: HflX; cd01878 998088010457 G1 box; other site 998088010458 GTP/Mg2+ binding site [chemical binding]; other site 998088010459 Switch I region; other site 998088010460 G2 box; other site 998088010461 G3 box; other site 998088010462 Switch II region; other site 998088010463 G4 box; other site 998088010464 G5 box; other site 998088010465 bacterial Hfq-like; Region: Hfq; cd01716 998088010466 hexamer interface [polypeptide binding]; other site 998088010467 Sm1 motif; other site 998088010468 RNA binding site [nucleotide binding]; other site 998088010469 Sm2 motif; other site 998088010470 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 998088010471 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 998088010472 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 998088010473 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 998088010474 ATP binding site [chemical binding]; other site 998088010475 Mg2+ binding site [ion binding]; other site 998088010476 G-X-G motif; other site 998088010477 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 998088010478 ATP binding site [chemical binding]; other site 998088010479 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 998088010480 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 998088010481 AMIN domain; Region: AMIN; pfam11741 998088010482 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 998088010483 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 998088010484 active site 998088010485 metal binding site [ion binding]; metal-binding site 998088010486 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088010487 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 998088010488 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088010489 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 998088010490 putative carbohydrate kinase; Provisional; Region: PRK10565 998088010491 Uncharacterized conserved protein [Function unknown]; Region: COG0062 998088010492 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 998088010493 putative substrate binding site [chemical binding]; other site 998088010494 putative ATP binding site [chemical binding]; other site 998088010495 epoxyqueuosine reductase; Region: TIGR00276 998088010496 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 998088010497 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 998088010498 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 998088010499 nucleotide binding site [chemical binding]; other site 998088010500 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 998088010501 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 998088010502 Walker A/P-loop; other site 998088010503 ATP binding site [chemical binding]; other site 998088010504 Q-loop/lid; other site 998088010505 ABC transporter signature motif; other site 998088010506 Walker B; other site 998088010507 D-loop; other site 998088010508 H-loop/switch region; other site 998088010509 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 998088010510 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 998088010511 dimer interface [polypeptide binding]; other site 998088010512 conserved gate region; other site 998088010513 ABC-ATPase subunit interface; other site 998088010514 NLPA lipoprotein; Region: Lipoprotein_9; cl17547 998088010515 DL-methionine transporter substrate-binding subunit; Provisional; Region: metQ; PRK11063 998088010516 transcriptional activator RfaH; Provisional; Region: rfaH; PRK09014 998088010517 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 998088010518 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 998088010519 heterodimer interface [polypeptide binding]; other site 998088010520 homodimer interface [polypeptide binding]; other site 998088010521 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 998088010522 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 998088010523 dimerization interface [polypeptide binding]; other site 998088010524 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088010525 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088010526 dimer interface [polypeptide binding]; other site 998088010527 putative CheW interface [polypeptide binding]; other site 998088010528 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 998088010529 Response regulator receiver domain; Region: Response_reg; pfam00072 998088010530 active site 998088010531 phosphorylation site [posttranslational modification] 998088010532 intermolecular recognition site; other site 998088010533 dimerization interface [polypeptide binding]; other site 998088010534 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 998088010535 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088010536 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 998088010537 substrate binding pocket [chemical binding]; other site 998088010538 membrane-bound complex binding site; other site 998088010539 hinge residues; other site 998088010540 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 998088010541 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 998088010542 putative active site [active] 998088010543 heme pocket [chemical binding]; other site 998088010544 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 998088010545 putative active site [active] 998088010546 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 998088010547 heme pocket [chemical binding]; other site 998088010548 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 998088010549 dimer interface [polypeptide binding]; other site 998088010550 phosphorylation site [posttranslational modification] 998088010551 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 998088010552 ATP binding site [chemical binding]; other site 998088010553 Mg2+ binding site [ion binding]; other site 998088010554 G-X-G motif; other site 998088010555 Response regulator receiver domain; Region: Response_reg; pfam00072 998088010556 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 998088010557 active site 998088010558 phosphorylation site [posttranslational modification] 998088010559 intermolecular recognition site; other site 998088010560 dimerization interface [polypeptide binding]; other site 998088010561 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 998088010562 putative binding surface; other site 998088010563 active site 998088010564 deoxyguanosinetriphosphate triphosphohydrolase; Provisional; Region: dgt; PRK04926 998088010565 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 998088010566 Zn2+ binding site [ion binding]; other site 998088010567 Mg2+ binding site [ion binding]; other site 998088010568 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 998088010569 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 998088010570 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 998088010571 putative active site [active] 998088010572 heme pocket [chemical binding]; other site 998088010573 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 998088010574 dimer interface [polypeptide binding]; other site 998088010575 phosphorylation site [posttranslational modification] 998088010576 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 998088010577 ATP binding site [chemical binding]; other site 998088010578 Mg2+ binding site [ion binding]; other site 998088010579 G-X-G motif; other site 998088010580 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 998088010581 active site 998088010582 phosphorylation site [posttranslational modification] 998088010583 intermolecular recognition site; other site 998088010584 dimerization interface [polypeptide binding]; other site 998088010585 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 998088010586 putative binding surface; other site 998088010587 active site 998088010588 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 998088010589 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 998088010590 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 998088010591 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 998088010592 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088010593 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088010594 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 998088010595 putative effector binding pocket; other site 998088010596 dimerization interface [polypeptide binding]; other site 998088010597 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 998088010598 Lin1944 and related proteins, classical (c) SDRs; Region: Lin1944_like_SDR_c; cd11731 998088010599 putative NAD(P) binding site [chemical binding]; other site 998088010600 homodimer interface [polypeptide binding]; other site 998088010601 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 998088010602 ATP binding site [chemical binding]; other site 998088010603 active site 998088010604 substrate binding site [chemical binding]; other site 998088010605 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 998088010606 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 998088010607 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 998088010608 dihydrodipicolinate synthase; Region: dapA; TIGR00674 998088010609 dimer interface [polypeptide binding]; other site 998088010610 active site 998088010611 catalytic residue [active] 998088010612 glycine cleavage system transcriptional repressor; Provisional; Region: gcvR; PRK11589 998088010613 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_1; cd04893 998088010614 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 998088010615 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 998088010616 catalytic triad [active] 998088010617 hypothetical protein; Validated; Region: PRK05445 998088010618 Protein of unknown function, DUF412; Region: DUF412; pfam04217 998088010619 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 998088010620 propionate/acetate kinase; Provisional; Region: PRK12379 998088010621 phosphate acetyltransferase; Reviewed; Region: PRK05632 998088010622 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 998088010623 DRTGG domain; Region: DRTGG; pfam07085 998088010624 phosphate acetyltransferase; Region: pta; TIGR00651 998088010625 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 998088010626 Helix-hairpin-helix motif; Region: HHH; pfam00633 998088010627 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 998088010628 active site 998088010629 tetramer interface; other site 998088010630 amino acid/peptide transporter (Peptide:H+ symporter), bacterial; Region: yjdL_sub1_fam; TIGR00924 998088010631 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 998088010632 putative substrate translocation pore; other site 998088010633 response regulator of RpoS; Provisional; Region: PRK10693 998088010634 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 998088010635 active site 998088010636 phosphorylation site [posttranslational modification] 998088010637 intermolecular recognition site; other site 998088010638 dimerization interface [polypeptide binding]; other site 998088010639 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; cl00120 998088010640 primosomal protein DnaI; Provisional; Region: PRK02854 998088010641 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 998088010642 NACHT domain; Region: NACHT; pfam05729 998088010643 Walker A motif; other site 998088010644 ATP binding site [chemical binding]; other site 998088010645 Walker B motif; other site 998088010646 atypical (a) SDRs, subgroup 5; Region: SDR_a5; cd05243 998088010647 NADH(P)-binding; Region: NAD_binding_10; pfam13460 998088010648 NAD(P) binding site [chemical binding]; other site 998088010649 putative active site [active] 998088010650 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 998088010651 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 998088010652 ABC-2 type transporter; Region: ABC2_membrane; cl17235 998088010653 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 998088010654 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 998088010655 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088010656 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088010657 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088010658 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 998088010659 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 998088010660 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 998088010661 FMN binding site [chemical binding]; other site 998088010662 active site 998088010663 catalytic residues [active] 998088010664 substrate binding site [chemical binding]; other site 998088010665 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 998088010666 global DNA-binding transcriptional dual regulator Fis; Provisional; Region: fis; PRK00430 998088010667 EamA-like transporter family; Region: EamA; pfam00892 998088010668 Protein of unknown function (DUF3100); Region: DUF3100; pfam11299 998088010669 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 998088010670 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 998088010671 metal binding site [ion binding]; metal-binding site 998088010672 dimer interface [polypeptide binding]; other site 998088010673 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 998088010674 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088010675 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 998088010676 substrate binding site [chemical binding]; other site 998088010677 dimerization interface [polypeptide binding]; other site 998088010678 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 998088010679 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 998088010680 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 998088010681 putative valine binding site [chemical binding]; other site 998088010682 dimer interface [polypeptide binding]; other site 998088010683 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 998088010684 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 998088010685 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 998088010686 PYR/PP interface [polypeptide binding]; other site 998088010687 dimer interface [polypeptide binding]; other site 998088010688 TPP binding site [chemical binding]; other site 998088010689 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 998088010690 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 998088010691 TPP-binding site [chemical binding]; other site 998088010692 dimer interface [polypeptide binding]; other site 998088010693 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 998088010694 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 998088010695 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 998088010696 active site 998088010697 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 998088010698 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088010699 2-isopropylmalate synthase; Validated; Region: PRK00915 998088010700 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 998088010701 active site 998088010702 catalytic residues [active] 998088010703 metal binding site [ion binding]; metal-binding site 998088010704 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 998088010705 tartrate dehydrogenase; Region: TTC; TIGR02089 998088010706 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 998088010707 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 998088010708 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 998088010709 substrate binding site [chemical binding]; other site 998088010710 ligand binding site [chemical binding]; other site 998088010711 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 998088010712 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 998088010713 substrate binding site [chemical binding]; other site 998088010714 Transglutaminase-like superfamily; Region: Transglut_core; cl17362 998088010715 PilZ domain; Region: PilZ; pfam07238 998088010716 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 998088010717 thiamine transporter substrate binding subunit; Provisional; Region: tbpA; PRK11205 998088010718 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 998088010719 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 998088010720 dimer interface [polypeptide binding]; other site 998088010721 conserved gate region; other site 998088010722 putative PBP binding loops; other site 998088010723 ABC-ATPase subunit interface; other site 998088010724 ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]; Region: ThiQ; COG3840 998088010725 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088010726 Walker A/P-loop; other site 998088010727 ATP binding site [chemical binding]; other site 998088010728 Q-loop/lid; other site 998088010729 ABC transporter signature motif; other site 998088010730 Walker B; other site 998088010731 D-loop; other site 998088010732 H-loop/switch region; other site 998088010733 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 998088010734 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 998088010735 putative active site [active] 998088010736 PhoH-like protein; Region: PhoH; pfam02562 998088010737 TSCPD domain; Region: TSCPD; pfam12637 998088010738 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 998088010739 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 998088010740 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 998088010741 active site 998088010742 dimer interface [polypeptide binding]; other site 998088010743 effector binding site; other site 998088010744 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 998088010745 Early set domain associated with the catalytic domain of pullulanase-like proteins; Region: E_set_pullulanase_like; cd02861 998088010746 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088010747 metal binding site [ion binding]; metal-binding site 998088010748 active site 998088010749 I-site; other site 998088010750 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 998088010751 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 998088010752 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 998088010753 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 998088010754 ring oligomerisation interface [polypeptide binding]; other site 998088010755 ATP/Mg binding site [chemical binding]; other site 998088010756 stacking interactions; other site 998088010757 hinge regions; other site 998088010758 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 998088010759 oligomerisation interface [polypeptide binding]; other site 998088010760 mobile loop; other site 998088010761 roof hairpin; other site 998088010762 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 998088010763 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_2; cd13149 998088010764 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 998088010765 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 998088010766 Aspartase; Region: Aspartase; cd01357 998088010767 active sites [active] 998088010768 tetramer interface [polypeptide binding]; other site 998088010769 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 998088010770 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK09412 998088010771 UGMP family protein; Validated; Region: PRK09604 998088010772 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 998088010773 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 998088010774 Yqey-like protein; Region: YqeY; pfam09424 998088010775 DNA primase; Validated; Region: dnaG; PRK05667 998088010776 CHC2 zinc finger; Region: zf-CHC2; pfam01807 998088010777 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 998088010778 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 998088010779 active site 998088010780 metal binding site [ion binding]; metal-binding site 998088010781 interdomain interaction site; other site 998088010782 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 998088010783 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 998088010784 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 998088010785 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 998088010786 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 998088010787 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 998088010788 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088010789 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 998088010790 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 998088010791 DNA binding residues [nucleotide binding] 998088010792 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 998088010793 Cytochrome b562; Region: Cytochrom_B562; cl01546 998088010794 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 998088010795 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 998088010796 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 998088010797 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 998088010798 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 998088010799 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 998088010800 purine monophosphate binding site [chemical binding]; other site 998088010801 dimer interface [polypeptide binding]; other site 998088010802 putative catalytic residues [active] 998088010803 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 998088010804 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 998088010805 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 998088010806 DNA binding residues [nucleotide binding] 998088010807 dimer interface [polypeptide binding]; other site 998088010808 metal binding site [ion binding]; metal-binding site 998088010809 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3036 998088010810 HemN family oxidoreductase; Provisional; Region: PRK05660 998088010811 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 998088010812 FeS/SAM binding site; other site 998088010813 HemN C-terminal domain; Region: HemN_C; pfam06969 998088010814 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 998088010815 active site 998088010816 dimerization interface [polypeptide binding]; other site 998088010817 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 998088010818 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 998088010819 putative substrate translocation pore; other site 998088010820 putative oxidoreductase; Provisional; Region: PRK11579 998088010821 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 998088010822 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 998088010823 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 998088010824 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 998088010825 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 998088010826 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 998088010827 Coenzyme A binding pocket [chemical binding]; other site 998088010828 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 998088010829 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 998088010830 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 998088010831 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 998088010832 active site 998088010833 Zn binding site [ion binding]; other site 998088010834 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 998088010835 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088010836 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088010837 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 998088010838 dimerization interface [polypeptide binding]; other site 998088010839 multidrug resistance protein MdtH; Provisional; Region: PRK11646 998088010840 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 998088010841 putative substrate translocation pore; other site 998088010842 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 998088010843 MarR family; Region: MarR; pfam01047 998088010844 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 998088010845 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 998088010846 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 998088010847 G1 box; other site 998088010848 putative GEF interaction site [polypeptide binding]; other site 998088010849 GTP/Mg2+ binding site [chemical binding]; other site 998088010850 Switch I region; other site 998088010851 G2 box; other site 998088010852 G3 box; other site 998088010853 Switch II region; other site 998088010854 G4 box; other site 998088010855 G5 box; other site 998088010856 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 998088010857 classical (c) SDRs; Region: SDR_c; cd05233 998088010858 short chain dehydrogenase; Provisional; Region: PRK07041 998088010859 NAD(P) binding site [chemical binding]; other site 998088010860 active site 998088010861 Tetratricopeptide repeat; Region: TPR_12; pfam13424 998088010862 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088010863 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088010864 metal binding site [ion binding]; metal-binding site 998088010865 active site 998088010866 I-site; other site 998088010867 hypothetical protein; Provisional; Region: yieM; PRK10997 998088010868 VWA YIEM type: 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...; Region: VWA_YIEM_type; cd01462 998088010869 metal ion-dependent adhesion site (MIDAS); other site 998088010870 regulatory ATPase RavA; Provisional; Region: PRK13531 998088010871 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 998088010872 Walker A motif; other site 998088010873 ATP binding site [chemical binding]; other site 998088010874 Walker B motif; other site 998088010875 arginine finger; other site 998088010876 Protein of unknown function (DUF3763); Region: DUF3763; pfam12592 998088010877 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 998088010878 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088010879 Coenzyme A binding pocket [chemical binding]; other site 998088010880 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 998088010881 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 998088010882 acyl-activating enzyme (AAE) consensus motif; other site 998088010883 putative AMP binding site [chemical binding]; other site 998088010884 putative active site [active] 998088010885 putative CoA binding site [chemical binding]; other site 998088010886 glutamate--cysteine ligase; Provisional; Region: PRK02107 998088010887 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 998088010888 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 998088010889 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 998088010890 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 998088010891 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 998088010892 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 998088010893 Predicted membrane protein [Function unknown]; Region: COG1238 998088010894 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 998088010895 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 998088010896 putative NAD(P) binding site [chemical binding]; other site 998088010897 ferredoxin-NADP reductase; Provisional; Region: PRK10926 998088010898 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 998088010899 FAD binding pocket [chemical binding]; other site 998088010900 FAD binding motif [chemical binding]; other site 998088010901 phosphate binding motif [ion binding]; other site 998088010902 beta-alpha-beta structure motif; other site 998088010903 NAD binding pocket [chemical binding]; other site 998088010904 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 998088010905 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 998088010906 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 998088010907 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 998088010908 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 998088010909 manganese transport protein MntH; Reviewed; Region: PRK00701 998088010910 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 998088010911 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 998088010912 Predicted membrane protein [Function unknown]; Region: COG4125 998088010913 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 998088010914 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 998088010915 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 998088010916 IHF dimer interface [polypeptide binding]; other site 998088010917 IHF - DNA interface [nucleotide binding]; other site 998088010918 anti-RNA polymerase sigma 70 factor; Provisional; Region: PRK11718 998088010919 PilZ domain; Region: PilZ; pfam07238 998088010920 DNA repair protein RadA; Provisional; Region: PRK11823 998088010921 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 998088010922 Walker A motif/ATP binding site; other site 998088010923 ATP binding site [chemical binding]; other site 998088010924 Walker B motif; other site 998088010925 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 998088010926 PilZ domain; Region: PilZ; pfam07238 998088010927 PilZ domain; Region: PilZ; pfam07238 998088010928 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 998088010929 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 998088010930 phosphoserine phosphatase SerB; Region: serB; TIGR00338 998088010931 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 998088010932 motif II; other site 998088010933 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 998088010934 purine nucleoside phosphorylase; Reviewed; Region: deoD; PRK05819 998088010935 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 998088010936 phosphopentomutase; Provisional; Region: PRK05362 998088010937 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 998088010938 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 998088010939 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 998088010940 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 998088010941 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 998088010942 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 998088010943 intersubunit interface [polypeptide binding]; other site 998088010944 active site 998088010945 catalytic residue [active] 998088010946 XapX domain; Region: XapX; TIGR03510 998088010947 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 998088010948 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 998088010949 Nucleoside recognition; Region: Gate; pfam07670 998088010950 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 998088010951 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 998088010952 active site 998088010953 S-ribosylhomocysteinase; Provisional; Region: PRK02260 998088010954 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 998088010955 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088010956 catalytic residue [active] 998088010957 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 998088010958 Nitrogen regulatory protein P-II; Region: P-II; smart00938 998088010959 NAD synthetase; Provisional; Region: PRK13981 998088010960 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 998088010961 multimer interface [polypeptide binding]; other site 998088010962 active site 998088010963 catalytic triad [active] 998088010964 protein interface 1 [polypeptide binding]; other site 998088010965 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 998088010966 homodimer interface [polypeptide binding]; other site 998088010967 NAD binding pocket [chemical binding]; other site 998088010968 ATP binding pocket [chemical binding]; other site 998088010969 Mg binding site [ion binding]; other site 998088010970 active-site loop [active] 998088010971 Type II transport protein GspH; Region: GspH; pfam12019 998088010972 Type II transport protein GspH; Region: GspH; pfam12019 998088010973 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 998088010974 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 998088010975 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 998088010976 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 998088010977 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 998088010978 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 998088010979 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 998088010980 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 998088010981 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 998088010982 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 998088010983 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 998088010984 lipoprotein signal peptidase; Provisional; Region: PRK14787 998088010985 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 998088010986 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 998088010987 active site 998088010988 HIGH motif; other site 998088010989 nucleotide binding site [chemical binding]; other site 998088010990 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 998088010991 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 998088010992 active site 998088010993 KMSKS motif; other site 998088010994 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 998088010995 tRNA binding surface [nucleotide binding]; other site 998088010996 anticodon binding site; other site 998088010997 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 998088010998 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 998088010999 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 998088011000 active site 998088011001 Riboflavin kinase; Region: Flavokinase; smart00904 998088011002 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 998088011003 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 998088011004 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 998088011005 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 998088011006 dimerization interface [polypeptide binding]; other site 998088011007 putative DNA binding site [nucleotide binding]; other site 998088011008 putative Zn2+ binding site [ion binding]; other site 998088011009 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 998088011010 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088011011 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 998088011012 putative dimerization interface [polypeptide binding]; other site 998088011013 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011014 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09561 998088011015 thymidylate synthase; Reviewed; Region: thyA; PRK01827 998088011016 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 998088011017 dimerization interface [polypeptide binding]; other site 998088011018 active site 998088011019 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 998088011020 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 998088011021 GAF domain; Region: GAF; pfam01590 998088011022 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 998088011023 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 998088011024 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 998088011025 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 998088011026 putative active site [active] 998088011027 Ap4A binding site [chemical binding]; other site 998088011028 nudix motif; other site 998088011029 putative metal binding site [ion binding]; other site 998088011030 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex. MutH...; Region: MutH_Sau3AI; cd00583 998088011031 putative DNA-binding cleft [nucleotide binding]; other site 998088011032 putative DNA clevage site; other site 998088011033 molecular lever; other site 998088011034 N-terminal Early set domain associated with the catalytic domain of isoamylase-like (also called glycogen 6-glucanohydrolase) proteins; Region: E_set_Isoamylase_like_N; cd07184 998088011035 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 998088011036 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 998088011037 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 998088011038 RimM N-terminal domain; Region: RimM; pfam01782 998088011039 PRC-barrel domain; Region: PRC; pfam05239 998088011040 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 998088011041 signal recognition particle protein; Provisional; Region: PRK10867 998088011042 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 998088011043 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 998088011044 P loop; other site 998088011045 GTP binding site [chemical binding]; other site 998088011046 Signal peptide binding domain; Region: SRP_SPB; pfam02978 998088011047 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4137 998088011048 hypothetical protein; Provisional; Region: PRK11573 998088011049 Domain of unknown function DUF21; Region: DUF21; pfam01595 998088011050 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 998088011051 Transporter associated domain; Region: CorC_HlyC; smart01091 998088011052 Predicted transcriptional regulator [Transcription]; Region: COG1959 998088011053 Transcriptional regulator; Region: Rrf2; cl17282 998088011054 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 998088011055 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 998088011056 heme-binding site [chemical binding]; other site 998088011057 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 998088011058 FAD binding pocket [chemical binding]; other site 998088011059 FAD binding motif [chemical binding]; other site 998088011060 phosphate binding motif [ion binding]; other site 998088011061 beta-alpha-beta structure motif; other site 998088011062 NAD binding pocket [chemical binding]; other site 998088011063 Heme binding pocket [chemical binding]; other site 998088011064 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 998088011065 malate dehydrogenase; Provisional; Region: PRK05086 998088011066 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 998088011067 NAD binding site [chemical binding]; other site 998088011068 dimerization interface [polypeptide binding]; other site 998088011069 Substrate binding site [chemical binding]; other site 998088011070 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 998088011071 dimer interface [polypeptide binding]; other site 998088011072 conserved gate region; other site 998088011073 putative PBP binding loops; other site 998088011074 ABC-ATPase subunit interface; other site 998088011075 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088011076 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 998088011077 dimer interface [polypeptide binding]; other site 998088011078 conserved gate region; other site 998088011079 putative PBP binding loops; other site 998088011080 ABC-ATPase subunit interface; other site 998088011081 putative ABC transporter arginine-biding protein; Provisional; Region: PRK15007 998088011082 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 998088011083 substrate binding pocket [chemical binding]; other site 998088011084 membrane-bound complex binding site; other site 998088011085 hinge residues; other site 998088011086 arginine transporter ATP-binding subunit; Provisional; Region: artP; PRK11124 998088011087 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088011088 Walker A/P-loop; other site 998088011089 ATP binding site [chemical binding]; other site 998088011090 Q-loop/lid; other site 998088011091 ABC transporter signature motif; other site 998088011092 Walker B; other site 998088011093 D-loop; other site 998088011094 H-loop/switch region; other site 998088011095 arginine repressor; Provisional; Region: PRK05066 998088011096 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 998088011097 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 998088011098 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 998088011099 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 998088011100 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088011101 Walker A/P-loop; other site 998088011102 ATP binding site [chemical binding]; other site 998088011103 Q-loop/lid; other site 998088011104 ABC transporter signature motif; other site 998088011105 Walker B; other site 998088011106 D-loop; other site 998088011107 H-loop/switch region; other site 998088011108 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 998088011109 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 998088011110 dimer interface [polypeptide binding]; other site 998088011111 conserved gate region; other site 998088011112 putative PBP binding loops; other site 998088011113 ABC-ATPase subunit interface; other site 998088011114 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 998088011115 dimer interface [polypeptide binding]; other site 998088011116 conserved gate region; other site 998088011117 putative PBP binding loops; other site 998088011118 ABC-ATPase subunit interface; other site 998088011119 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 998088011120 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 998088011121 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 998088011122 Nitrogen regulatory protein P-II; Region: P-II; smart00938 998088011123 hypothetical protein; Provisional; Region: PRK09256 998088011124 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 998088011125 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 998088011126 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 998088011127 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 998088011128 DNA binding site [nucleotide binding] 998088011129 active site 998088011130 hypothetical protein; Validated; Region: PRK02101 998088011131 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 998088011132 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 998088011133 Walker A motif; other site 998088011134 ATP binding site [chemical binding]; other site 998088011135 Walker B motif; other site 998088011136 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 998088011137 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 998088011138 Walker A motif; other site 998088011139 ATP binding site [chemical binding]; other site 998088011140 Walker B motif; other site 998088011141 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 998088011142 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 998088011143 catalytic residue [active] 998088011144 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 998088011145 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 998088011146 YGGT family; Region: YGGT; pfam02325 998088011147 YGGT family; Region: YGGT; pfam02325 998088011148 hypothetical protein; Validated; Region: PRK05090 998088011149 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 998088011150 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 998088011151 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 998088011152 Nucleoside recognition; Region: Gate; pfam07670 998088011153 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 998088011154 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088011155 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088011156 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 998088011157 putative effector binding pocket; other site 998088011158 dimerization interface [polypeptide binding]; other site 998088011159 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 998088011160 catalytic residues [active] 998088011161 dimer interface [polypeptide binding]; other site 998088011162 NnrU protein; Region: NnrU; pfam07298 998088011163 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 998088011164 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 998088011165 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 998088011166 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 998088011167 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 998088011168 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 998088011169 Uncharacterized protein family (UPF0231); Region: UPF0231; pfam06062 998088011170 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 998088011171 substrate binding pocket [chemical binding]; other site 998088011172 membrane-bound complex binding site; other site 998088011173 hinge residues; other site 998088011174 CAAX protease self-immunity; Region: Abi; pfam02517 998088011175 Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine; Region: nSMase; cd09078 998088011176 putative catalytic site [active] 998088011177 metal binding site A [ion binding]; metal-binding site 998088011178 phosphate binding site [ion binding]; other site 998088011179 metal binding site C [ion binding]; metal-binding site 998088011180 metal binding site B [ion binding]; metal-binding site 998088011181 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 998088011182 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; cl17251 998088011183 ATP binding site [chemical binding]; other site 998088011184 putative Mg++ binding site [ion binding]; other site 998088011185 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 998088011186 nucleotide binding region [chemical binding]; other site 998088011187 ATP-binding site [chemical binding]; other site 998088011188 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 998088011189 substrate binding pocket [chemical binding]; other site 998088011190 membrane-bound complex binding site; other site 998088011191 hinge residues; other site 998088011192 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 998088011193 dimer interface [polypeptide binding]; other site 998088011194 catalytic triad [active] 998088011195 peroxidatic and resolving cysteines [active] 998088011196 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 998088011197 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 998088011198 metal-binding site [ion binding] 998088011199 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 998088011200 Soluble P-type ATPase [General function prediction only]; Region: COG4087 998088011201 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cd10315 998088011202 carbohydrate binding site [chemical binding]; other site 998088011203 alpha-1,6-glucosidases, pullulanase-type; Region: pullul_strch; TIGR02103 998088011204 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 998088011205 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 998088011206 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 998088011207 active site 998088011208 active site 998088011209 catalytic site [active] 998088011210 Domain of unknown function (DUF3372); Region: DUF3372; pfam11852 998088011211 Early set domain associated with the catalytic domain of pullulanase-like proteins; Region: E_set_pullulanase_like; cd02861 998088011212 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 998088011213 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 998088011214 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 998088011215 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 998088011216 putative metal binding site [ion binding]; other site 998088011217 putative homodimer interface [polypeptide binding]; other site 998088011218 putative homotetramer interface [polypeptide binding]; other site 998088011219 putative homodimer-homodimer interface [polypeptide binding]; other site 998088011220 putative allosteric switch controlling residues; other site 998088011221 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 998088011222 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 998088011223 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088011224 homodimer interface [polypeptide binding]; other site 998088011225 catalytic residue [active] 998088011226 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088011227 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088011228 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 998088011229 substrate binding pocket [chemical binding]; other site 998088011230 dimerization interface [polypeptide binding]; other site 998088011231 Domain of unknown function (DUF1820); Region: DUF1820; pfam08850 998088011232 glycine radical enzyme activase, YjjW family; Region: activase_YjjW; TIGR04041 998088011233 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 998088011234 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 998088011235 hypothetical protein; Provisional; Region: PRK10977 998088011236 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 998088011237 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 998088011238 AzlC protein; Region: AzlC; pfam03591 998088011239 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 998088011240 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 998088011241 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 998088011242 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 998088011243 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 998088011244 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 998088011245 protein binding site [polypeptide binding]; other site 998088011246 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 998088011247 Domain interface; other site 998088011248 Peptide binding site; other site 998088011249 Active site tetrad [active] 998088011250 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 998088011251 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 998088011252 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 998088011253 FAD binding pocket [chemical binding]; other site 998088011254 FAD binding motif [chemical binding]; other site 998088011255 phosphate binding motif [ion binding]; other site 998088011256 beta-alpha-beta structure motif; other site 998088011257 NAD binding pocket [chemical binding]; other site 998088011258 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 998088011259 PTS_IIA, PTS system, glucose/sucrose 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_glc; cl00162 998088011260 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 998088011261 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 998088011262 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 998088011263 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 998088011264 DXD motif; other site 998088011265 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 998088011266 Peptidase M3-like family, a zincin metallopeptidase, includes M3 and M32 families; Region: M3_like; cd06258 998088011267 active site 998088011268 Zn binding site [ion binding]; other site 998088011269 Cache domain; Region: Cache_2; pfam08269 998088011270 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 998088011271 dimerization interface [polypeptide binding]; other site 998088011272 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088011273 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088011274 dimer interface [polypeptide binding]; other site 998088011275 putative CheW interface [polypeptide binding]; other site 998088011276 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 998088011277 Chitin binding domain; Region: Chitin_bind_3; pfam03067 998088011278 Predicted membrane protein [Function unknown]; Region: COG3174 998088011279 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 998088011280 maltose O-acetyltransferase; Provisional; Region: PRK10092 998088011281 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 998088011282 active site 998088011283 substrate binding site [chemical binding]; other site 998088011284 trimer interface [polypeptide binding]; other site 998088011285 CoA binding site [chemical binding]; other site 998088011286 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 998088011287 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 998088011288 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 998088011289 motif II; other site 998088011290 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 998088011291 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 998088011292 dimer interface [polypeptide binding]; other site 998088011293 ADP-ribose binding site [chemical binding]; other site 998088011294 active site 998088011295 nudix motif; other site 998088011296 metal binding site [ion binding]; metal-binding site 998088011297 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 998088011298 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 998088011299 active site 998088011300 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 998088011301 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 998088011302 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 998088011303 dimer interface [polypeptide binding]; other site 998088011304 putative tRNA-binding site [nucleotide binding]; other site 998088011305 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 998088011306 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 998088011307 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088011308 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox'...; Region: Met_repressor_MetJ; cd00490 998088011309 dimerization interface [polypeptide binding]; other site 998088011310 DNA binding site [nucleotide binding] 998088011311 corepressor binding sites; other site 998088011312 O-succinylhomoserine (thiol)-lyase; Region: O_succ_thio_ly; TIGR02080 998088011313 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 998088011314 homodimer interface [polypeptide binding]; other site 998088011315 substrate-cofactor binding pocket; other site 998088011316 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088011317 catalytic residue [active] 998088011318 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 998088011319 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 998088011320 nucleotide binding site [chemical binding]; other site 998088011321 substrate binding site [chemical binding]; other site 998088011322 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 998088011323 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 998088011324 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 998088011325 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 998088011326 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 998088011327 Uncharacterized conserved protein [Function unknown]; Region: COG3025 998088011328 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 998088011329 putative active site [active] 998088011330 putative metal binding residues [ion binding]; other site 998088011331 signature motif; other site 998088011332 putative triphosphate binding site [ion binding]; other site 998088011333 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 998088011334 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 998088011335 dimer interface [polypeptide binding]; other site 998088011336 active site 998088011337 catalytic residue [active] 998088011338 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 998088011339 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 998088011340 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 998088011341 S-adenosylmethionine binding site [chemical binding]; other site 998088011342 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00844 998088011343 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 998088011344 ligand binding site; other site 998088011345 oligomer interface; other site 998088011346 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 998088011347 dimer interface [polypeptide binding]; other site 998088011348 N-terminal domain interface [polypeptide binding]; other site 998088011349 sulfate 1 binding site; other site 998088011350 glycogen synthase; Provisional; Region: glgA; PRK00654 998088011351 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 998088011352 ADP-binding pocket [chemical binding]; other site 998088011353 homodimer interface [polypeptide binding]; other site 998088011354 Late competence development protein ComFB; Region: ComFB; pfam10719 998088011355 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 998088011356 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 998088011357 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 998088011358 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 998088011359 Cl- selectivity filter; other site 998088011360 Cl- binding residues [ion binding]; other site 998088011361 pore gating glutamate residue; other site 998088011362 dimer interface [polypeptide binding]; other site 998088011363 H+/Cl- coupling transport residue; other site 998088011364 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 998088011365 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 998088011366 inhibitor-cofactor binding pocket; inhibition site 998088011367 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088011368 catalytic residue [active] 998088011369 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 998088011370 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 998088011371 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 998088011372 catalytic residues [active] 998088011373 ATP-dependent helicase HepA; Validated; Region: PRK04914 998088011374 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 998088011375 ATP binding site [chemical binding]; other site 998088011376 putative Mg++ binding site [ion binding]; other site 998088011377 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 998088011378 nucleotide binding region [chemical binding]; other site 998088011379 ATP-binding site [chemical binding]; other site 998088011380 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 998088011381 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 998088011382 active site 998088011383 maltose O-acetyltransferase; Provisional; Region: PRK10092 998088011384 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 998088011385 active site 998088011386 substrate binding site [chemical binding]; other site 998088011387 trimer interface [polypeptide binding]; other site 998088011388 CoA binding site [chemical binding]; other site 998088011389 trehalose-6-phosphate hydrolase; Provisional; Region: PRK10933 998088011390 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 998088011391 Ca binding site [ion binding]; other site 998088011392 active site 998088011393 catalytic site [active] 998088011394 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 998088011395 PTS system trehalose(maltose)-specific transporter subunits IIBC; Provisional; Region: PRK11007 998088011396 PTS_IIB, PTS system, glucose/sucrose specific IIB 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_IIB_glc; cd00212 998088011397 active site turn [active] 998088011398 phosphorylation site [posttranslational modification] 998088011399 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 998088011400 trehalose repressor; Provisional; Region: treR; PRK09492 998088011401 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088011402 DNA binding site [nucleotide binding] 998088011403 domain linker motif; other site 998088011404 Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_TreR_like; cd01542 998088011405 dimerization interface [polypeptide binding]; other site 998088011406 ligand binding site [chemical binding]; other site 998088011407 Predicted permeases [General function prediction only]; Region: COG0679 998088011408 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 998088011409 metal-binding site [ion binding] 998088011410 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cd00411 998088011411 active site 998088011412 homodimer interface [polypeptide binding]; other site 998088011413 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 998088011414 Domain of unknown function DUF21; Region: DUF21; pfam01595 998088011415 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 998088011416 Transporter associated domain; Region: CorC_HlyC; smart01091 998088011417 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 998088011418 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 998088011419 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 998088011420 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 998088011421 carbon storage regulator; Provisional; Region: PRK01712 998088011422 aspartate kinase; Reviewed; Region: PRK06635 998088011423 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 998088011424 putative nucleotide binding site [chemical binding]; other site 998088011425 putative catalytic residues [active] 998088011426 putative Mg ion binding site [ion binding]; other site 998088011427 putative aspartate binding site [chemical binding]; other site 998088011428 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 998088011429 putative allosteric regulatory site; other site 998088011430 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 998088011431 putative allosteric regulatory residue; other site 998088011432 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 998088011433 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 998088011434 motif 1; other site 998088011435 active site 998088011436 motif 2; other site 998088011437 motif 3; other site 998088011438 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 998088011439 DHHA1 domain; Region: DHHA1; pfam02272 998088011440 recombination regulator RecX; Reviewed; Region: recX; PRK00117 998088011441 recombinase A; Provisional; Region: recA; PRK09354 998088011442 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 998088011443 hexamer interface [polypeptide binding]; other site 998088011444 Walker A motif; other site 998088011445 ATP binding site [chemical binding]; other site 998088011446 Walker B motif; other site 998088011447 Competence-damaged protein; Region: CinA; cl00666 998088011448 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 998088011449 MutS domain I; Region: MutS_I; pfam01624 998088011450 MutS domain II; Region: MutS_II; pfam05188 998088011451 MutS domain III; Region: MutS_III; pfam05192 998088011452 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 998088011453 Walker A/P-loop; other site 998088011454 ATP binding site [chemical binding]; other site 998088011455 Q-loop/lid; other site 998088011456 ABC transporter signature motif; other site 998088011457 Walker B; other site 998088011458 D-loop; other site 998088011459 H-loop/switch region; other site 998088011460 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 998088011461 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 998088011462 active site 998088011463 nucleophile elbow; other site 998088011464 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 998088011465 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 998088011466 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088011467 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088011468 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 998088011469 putative dimerization interface [polypeptide binding]; other site 998088011470 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 998088011471 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 998088011472 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 998088011473 putative deacylase active site [active] 998088011474 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 998088011475 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 998088011476 Coenzyme A binding pocket [chemical binding]; other site 998088011477 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 998088011478 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 998088011479 non-specific DNA binding site [nucleotide binding]; other site 998088011480 salt bridge; other site 998088011481 sequence-specific DNA binding site [nucleotide binding]; other site 998088011482 Domain of unknown function (DUF955); Region: DUF955; cl01076 998088011483 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 998088011484 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 998088011485 FeS/SAM binding site; other site 998088011486 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 998088011487 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 998088011488 ThiS interaction site; other site 998088011489 putative active site [active] 998088011490 tetramer interface [polypeptide binding]; other site 998088011491 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 998088011492 thiS-thiF/thiG interaction site; other site 998088011493 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 998088011494 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 998088011495 ATP binding site [chemical binding]; other site 998088011496 substrate interface [chemical binding]; other site 998088011497 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 998088011498 dimer interface [polypeptide binding]; other site 998088011499 HMP-P kinase/thiamin-monophosphate pyrophosphorylase; Region: PLN02898 998088011500 substrate binding site [chemical binding]; other site 998088011501 ATP binding site [chemical binding]; other site 998088011502 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 998088011503 thiamine phosphate binding site [chemical binding]; other site 998088011504 active site 998088011505 pyrophosphate binding site [ion binding]; other site 998088011506 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 998088011507 ThiC-associated domain; Region: ThiC-associated; pfam13667 998088011508 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 998088011509 Aerolysin/Pertussis toxin (APT) domain; Region: APT; pfam03440 998088011510 Aerolysin toxin; Region: Aerolysin; pfam01117 998088011511 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088011512 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 998088011513 active site 998088011514 phosphorylation site [posttranslational modification] 998088011515 intermolecular recognition site; other site 998088011516 dimerization interface [polypeptide binding]; other site 998088011517 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 998088011518 DNA binding site [nucleotide binding] 998088011519 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088011520 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 998088011521 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 998088011522 RimK-like ATP-grasp domain; Region: RimK; pfam08443 998088011523 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 998088011524 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 998088011525 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 998088011526 substrate binding pocket [chemical binding]; other site 998088011527 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 998088011528 B12 binding site [chemical binding]; other site 998088011529 cobalt ligand [ion binding]; other site 998088011530 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 998088011531 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 998088011532 Transcriptional regulators [Transcription]; Region: PurR; COG1609 998088011533 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088011534 DNA binding site [nucleotide binding] 998088011535 domain linker motif; other site 998088011536 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 998088011537 dimerization interface (closed form) [polypeptide binding]; other site 998088011538 ligand binding site [chemical binding]; other site 998088011539 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 998088011540 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 998088011541 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 998088011542 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088011543 homodimer interface [polypeptide binding]; other site 998088011544 catalytic residue [active] 998088011545 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 998088011546 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 998088011547 HDOD domain; Region: HDOD; pfam08668 998088011548 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 998088011549 acid phosphatase/phosphotransferase; Provisional; Region: aphA; PRK11009 998088011550 Predicted ATPases of PP-loop superfamily [General function prediction only]; Region: COG2102 998088011551 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_IV; cd01994 998088011552 Ligand Binding Site [chemical binding]; other site 998088011553 metabolite-proton symporter; Region: 2A0106; TIGR00883 998088011554 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 998088011555 putative substrate translocation pore; other site 998088011556 inner membrane protein; Provisional; Region: PRK10995 998088011557 protease TldD; Provisional; Region: tldD; PRK10735 998088011558 Predicted amidohydrolase [General function prediction only]; Region: COG0388 998088011559 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 998088011560 putative active site [active] 998088011561 catalytic triad [active] 998088011562 dimer interface [polypeptide binding]; other site 998088011563 TIGR02099 family protein; Region: TIGR02099 998088011564 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 998088011565 ribonuclease G; Provisional; Region: PRK11712 998088011566 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 998088011567 homodimer interface [polypeptide binding]; other site 998088011568 oligonucleotide binding site [chemical binding]; other site 998088011569 Maf-like protein; Region: Maf; pfam02545 998088011570 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 998088011571 active site 998088011572 dimer interface [polypeptide binding]; other site 998088011573 rod shape-determining protein MreD; Region: MreD; cl01087 998088011574 rod shape-determining protein MreC; Region: mreC; TIGR00219 998088011575 rod shape-determining protein MreC; Region: MreC; pfam04085 998088011576 rod shape-determining protein MreB; Provisional; Region: PRK13927 998088011577 MreB and similar proteins; Region: MreB_like; cd10225 998088011578 nucleotide binding site [chemical binding]; other site 998088011579 Mg binding site [ion binding]; other site 998088011580 putative protofilament interaction site [polypeptide binding]; other site 998088011581 RodZ interaction site [polypeptide binding]; other site 998088011582 legume lectins; Region: lectin_L-type; cl14058 998088011583 homotetramer interaction site [polypeptide binding]; other site 998088011584 homodimer interaction site [polypeptide binding]; other site 998088011585 carbohydrate binding site [chemical binding]; other site 998088011586 metal binding site [ion binding]; metal-binding site 998088011587 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 998088011588 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 998088011589 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 998088011590 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 998088011591 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 998088011592 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 998088011593 Walker A motif; other site 998088011594 ATP binding site [chemical binding]; other site 998088011595 Walker B motif; other site 998088011596 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 998088011597 binding surface 998088011598 TPR motif; other site 998088011599 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 998088011600 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 998088011601 Walker A motif; other site 998088011602 ATP binding site [chemical binding]; other site 998088011603 Walker B motif; other site 998088011604 arginine finger; other site 998088011605 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 998088011606 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 998088011607 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 998088011608 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 998088011609 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 998088011610 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 998088011611 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 998088011612 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 998088011613 catalytic residue [active] 998088011614 regulatory protein CsrD; Provisional; Region: PRK11059 998088011615 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088011616 metal binding site [ion binding]; metal-binding site 998088011617 active site 998088011618 I-site; other site 998088011619 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 998088011620 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 998088011621 calcium/sodium:proton antiporter; Provisional; Region: PRK10599 998088011622 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 998088011623 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 998088011624 active sites [active] 998088011625 tetramer interface [polypeptide binding]; other site 998088011626 urocanate hydratase; Provisional; Region: PRK05414 998088011627 formimidoylglutamase; Provisional; Region: PRK13775 998088011628 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 998088011629 putative active site [active] 998088011630 putative metal binding site [ion binding]; other site 998088011631 imidazolonepropionase; Validated; Region: PRK09356 998088011632 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 998088011633 active site 998088011634 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 998088011635 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088011636 DNA-binding site [nucleotide binding]; DNA binding site 998088011637 UTRA domain; Region: UTRA; pfam07702 998088011638 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 998088011639 active site clefts [active] 998088011640 zinc binding site [ion binding]; other site 998088011641 dimer interface [polypeptide binding]; other site 998088011642 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 998088011643 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 998088011644 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 998088011645 DNA binding residues [nucleotide binding] 998088011646 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 998088011647 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 998088011648 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 998088011649 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 998088011650 Walker A/P-loop; other site 998088011651 ATP binding site [chemical binding]; other site 998088011652 Q-loop/lid; other site 998088011653 ABC transporter signature motif; other site 998088011654 Walker B; other site 998088011655 D-loop; other site 998088011656 H-loop/switch region; other site 998088011657 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 998088011658 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 998088011659 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 998088011660 P loop; other site 998088011661 GTP binding site [chemical binding]; other site 998088011662 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 998088011663 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 998088011664 S-adenosylmethionine binding site [chemical binding]; other site 998088011665 Protein of unknown function (DUF1145); Region: DUF1145; pfam06611 998088011666 Predicted transcriptional regulator [Transcription]; Region: COG2378 998088011667 WYL domain; Region: WYL; pfam13280 998088011668 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 998088011669 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 998088011670 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 998088011671 TrkA-N domain; Region: TrkA_N; pfam02254 998088011672 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 998088011673 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088011674 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088011675 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 998088011676 dimerization interface [polypeptide binding]; other site 998088011677 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 998088011678 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011679 NAD(P) binding site [chemical binding]; other site 998088011680 active site 998088011681 Predicted metal-binding protein [General function prediction only]; Region: COG3019 998088011682 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 998088011683 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 998088011684 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 998088011685 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 998088011686 TRAP-type uncharacterized transport system, fused permease components [General function prediction only]; Region: COG4666 998088011687 TRAP-type uncharacterized transport system, fused permease components [General function prediction only]; Region: COG4666 998088011688 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 998088011689 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 998088011690 PLD-like domain; Region: PLDc_2; pfam13091 998088011691 putative active site [active] 998088011692 catalytic site [active] 998088011693 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 998088011694 PLD-like domain; Region: PLDc_2; pfam13091 998088011695 putative active site [active] 998088011696 catalytic site [active] 998088011697 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 998088011698 substrate binding pocket [chemical binding]; other site 998088011699 membrane-bound complex binding site; other site 998088011700 hinge residues; other site 998088011701 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 998088011702 N-acetyl-D-glucosamine binding site [chemical binding]; other site 998088011703 catalytic residue [active] 998088011704 Protein of unknown function (DUF406); Region: DUF406; pfam04175 998088011705 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 998088011706 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 998088011707 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088011708 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 998088011709 substrate binding pocket [chemical binding]; other site 998088011710 dimerization interface [polypeptide binding]; other site 998088011711 MarC family integral membrane protein; Region: MarC; cl00919 998088011712 probable metal-binding protein; Region: matur_matur; TIGR03853 998088011713 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 998088011714 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 998088011715 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 998088011716 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088011717 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088011718 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 998088011719 putative effector binding pocket; other site 998088011720 dimerization interface [polypeptide binding]; other site 998088011721 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 998088011722 HlyD family secretion protein; Region: HlyD; pfam00529 998088011723 HlyD family secretion protein; Region: HlyD_3; pfam13437 998088011724 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 998088011725 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 998088011726 putative substrate translocation pore; other site 998088011727 YhhN-like protein; Region: YhhN; pfam07947 998088011728 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 998088011729 Di-iron ligands [ion binding]; other site 998088011730 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 998088011731 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 998088011732 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088011733 hypothetical protein; Provisional; Region: PRK11056 998088011734 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 998088011735 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 998088011736 active site 998088011737 motif I; other site 998088011738 motif II; other site 998088011739 elongation factor Tu; Reviewed; Region: PRK00049 998088011740 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 998088011741 G1 box; other site 998088011742 GEF interaction site [polypeptide binding]; other site 998088011743 GTP/Mg2+ binding site [chemical binding]; other site 998088011744 Switch I region; other site 998088011745 G2 box; other site 998088011746 G3 box; other site 998088011747 Switch II region; other site 998088011748 G4 box; other site 998088011749 G5 box; other site 998088011750 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 998088011751 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 998088011752 Antibiotic Binding Site [chemical binding]; other site 998088011753 elongation factor G; Reviewed; Region: PRK00007 998088011754 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 998088011755 G1 box; other site 998088011756 putative GEF interaction site [polypeptide binding]; other site 998088011757 GTP/Mg2+ binding site [chemical binding]; other site 998088011758 Switch I region; other site 998088011759 G2 box; other site 998088011760 G3 box; other site 998088011761 Switch II region; other site 998088011762 G4 box; other site 998088011763 G5 box; other site 998088011764 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 998088011765 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 998088011766 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 998088011767 30S ribosomal protein S7; Validated; Region: PRK05302 998088011768 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 998088011769 S17 interaction site [polypeptide binding]; other site 998088011770 S8 interaction site; other site 998088011771 16S rRNA interaction site [nucleotide binding]; other site 998088011772 streptomycin interaction site [chemical binding]; other site 998088011773 23S rRNA interaction site [nucleotide binding]; other site 998088011774 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 998088011775 sulfur relay protein TusB/DsrH; Region: sulf_tusB_dsrH; TIGR03011 998088011776 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 998088011777 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 998088011778 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 998088011779 homotrimer interaction site [polypeptide binding]; other site 998088011780 putative active site [active] 998088011781 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 998088011782 YheO-like PAS domain; Region: PAS_6; pfam08348 998088011783 HTH domain; Region: HTH_22; pfam13309 998088011784 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 998088011785 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 998088011786 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 998088011787 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 998088011788 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 998088011789 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 998088011790 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 998088011791 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 998088011792 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 998088011793 DNA binding site [nucleotide binding] 998088011794 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 998088011795 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 998088011796 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 998088011797 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 998088011798 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 998088011799 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 998088011800 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 998088011801 RPB3 interaction site [polypeptide binding]; other site 998088011802 RPB1 interaction site [polypeptide binding]; other site 998088011803 RPB11 interaction site [polypeptide binding]; other site 998088011804 RPB10 interaction site [polypeptide binding]; other site 998088011805 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 998088011806 core dimer interface [polypeptide binding]; other site 998088011807 peripheral dimer interface [polypeptide binding]; other site 998088011808 L10 interface [polypeptide binding]; other site 998088011809 L11 interface [polypeptide binding]; other site 998088011810 putative EF-Tu interaction site [polypeptide binding]; other site 998088011811 putative EF-G interaction site [polypeptide binding]; other site 998088011812 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 998088011813 23S rRNA interface [nucleotide binding]; other site 998088011814 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 998088011815 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 998088011816 mRNA/rRNA interface [nucleotide binding]; other site 998088011817 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 998088011818 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 998088011819 23S rRNA interface [nucleotide binding]; other site 998088011820 L7/L12 interface [polypeptide binding]; other site 998088011821 putative thiostrepton binding site; other site 998088011822 L25 interface [polypeptide binding]; other site 998088011823 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 998088011824 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 998088011825 putative homodimer interface [polypeptide binding]; other site 998088011826 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 998088011827 heterodimer interface [polypeptide binding]; other site 998088011828 homodimer interface [polypeptide binding]; other site 998088011829 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 998088011830 elongation factor Tu; Reviewed; Region: PRK00049 998088011831 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 998088011832 G1 box; other site 998088011833 GEF interaction site [polypeptide binding]; other site 998088011834 GTP/Mg2+ binding site [chemical binding]; other site 998088011835 Switch I region; other site 998088011836 G2 box; other site 998088011837 G3 box; other site 998088011838 Switch II region; other site 998088011839 G4 box; other site 998088011840 G5 box; other site 998088011841 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 998088011842 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 998088011843 Antibiotic Binding Site [chemical binding]; other site 998088011844 pantothenate kinase; Provisional; Region: PRK05439 998088011845 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point...; Region: PanK; cd02025 998088011846 ATP-binding site [chemical binding]; other site 998088011847 CoA-binding site [chemical binding]; other site 998088011848 Mg2+-binding site [ion binding]; other site 998088011849 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 998088011850 putative DNA binding site [nucleotide binding]; other site 998088011851 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 998088011852 putative Zn2+ binding site [ion binding]; other site 998088011853 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 998088011854 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 998088011855 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 998088011856 FAD binding domain; Region: FAD_binding_4; pfam01565 998088011857 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 998088011858 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 998088011859 TrkA-N domain; Region: TrkA_N; pfam02254 998088011860 TrkA-C domain; Region: TrkA_C; pfam02080 998088011861 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 998088011862 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 998088011863 Cupin; Region: Cupin_6; pfam12852 998088011864 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088011865 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 998088011866 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 998088011867 Protein of unknown function, DUF417; Region: DUF417; cl01162 998088011868 DNA topoisomerase III; Provisional; Region: PRK07726 998088011869 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 998088011870 active site 998088011871 putative interdomain interaction site [polypeptide binding]; other site 998088011872 putative metal-binding site [ion binding]; other site 998088011873 putative nucleotide binding site [chemical binding]; other site 998088011874 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 998088011875 domain I; other site 998088011876 DNA binding groove [nucleotide binding] 998088011877 phosphate binding site [ion binding]; other site 998088011878 domain II; other site 998088011879 domain III; other site 998088011880 nucleotide binding site [chemical binding]; other site 998088011881 catalytic site [active] 998088011882 domain IV; other site 998088011883 Response regulator receiver domain; Region: Response_reg; pfam00072 998088011884 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 998088011885 active site 998088011886 phosphorylation site [posttranslational modification] 998088011887 intermolecular recognition site; other site 998088011888 dimerization interface [polypeptide binding]; other site 998088011889 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 998088011890 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 998088011891 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 998088011892 ligand binding site [chemical binding]; other site 998088011893 flexible hinge region; other site 998088011894 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 998088011895 dimer interface [polypeptide binding]; other site 998088011896 phosphorylation site [posttranslational modification] 998088011897 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 998088011898 ATP binding site [chemical binding]; other site 998088011899 Mg2+ binding site [ion binding]; other site 998088011900 G-X-G motif; other site 998088011901 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 998088011902 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 998088011903 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 998088011904 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 998088011905 molybdopterin cofactor binding site [chemical binding]; other site 998088011906 substrate binding site [chemical binding]; other site 998088011907 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 998088011908 molybdopterin cofactor binding site; other site 998088011909 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088011910 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 998088011911 ATP binding site [chemical binding]; other site 998088011912 Mg2+ binding site [ion binding]; other site 998088011913 G-X-G motif; other site 998088011914 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088011915 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 998088011916 active site 998088011917 phosphorylation site [posttranslational modification] 998088011918 intermolecular recognition site; other site 998088011919 dimerization interface [polypeptide binding]; other site 998088011920 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 998088011921 DNA binding site [nucleotide binding] 998088011922 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 998088011923 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 998088011924 TMAO/DMSO reductase; Reviewed; Region: PRK05363 998088011925 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 998088011926 Moco binding site; other site 998088011927 metal coordination site [ion binding]; other site 998088011928 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 998088011929 response regulator GlrR; Provisional; Region: PRK15115 998088011930 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 998088011931 active site 998088011932 phosphorylation site [posttranslational modification] 998088011933 intermolecular recognition site; other site 998088011934 dimerization interface [polypeptide binding]; other site 998088011935 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 998088011936 Walker A motif; other site 998088011937 ATP binding site [chemical binding]; other site 998088011938 Walker B motif; other site 998088011939 arginine finger; other site 998088011940 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 998088011941 HAMP domain; Region: HAMP; pfam00672 998088011942 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 998088011943 dimer interface [polypeptide binding]; other site 998088011944 phosphorylation site [posttranslational modification] 998088011945 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 998088011946 ATP binding site [chemical binding]; other site 998088011947 Mg2+ binding site [ion binding]; other site 998088011948 G-X-G motif; other site 998088011949 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 998088011950 dihydromonapterin reductase; Provisional; Region: PRK06483 998088011951 NAD(P) binding site [chemical binding]; other site 998088011952 active site 998088011953 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_16; cd04629 998088011954 Uncharacterized integral membrane protein (DUF2301); Region: DUF2301; pfam10063 998088011955 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088011956 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 998088011957 substrate binding pocket [chemical binding]; other site 998088011958 membrane-bound complex binding site; other site 998088011959 hinge residues; other site 998088011960 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 998088011961 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 998088011962 putative DNA binding site [nucleotide binding]; other site 998088011963 putative Zn2+ binding site [ion binding]; other site 998088011964 AsnC family; Region: AsnC_trans_reg; pfam01037 998088011965 asparagine synthetase AsnA; Provisional; Region: PRK05425 998088011966 motif 1; other site 998088011967 dimer interface [polypeptide binding]; other site 998088011968 active site 998088011969 motif 2; other site 998088011970 motif 3; other site 998088011971 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 998088011972 Clp amino terminal domain; Region: Clp_N; pfam02861 998088011973 Clp amino terminal domain; Region: Clp_N; pfam02861 998088011974 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 998088011975 Walker A motif; other site 998088011976 ATP binding site [chemical binding]; other site 998088011977 Walker B motif; other site 998088011978 arginine finger; other site 998088011979 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 998088011980 Walker A motif; other site 998088011981 ATP binding site [chemical binding]; other site 998088011982 Walker B motif; other site 998088011983 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 998088011984 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 998088011985 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 998088011986 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 998088011987 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 998088011988 RNA binding surface [nucleotide binding]; other site 998088011989 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 998088011990 active site 998088011991 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 998088011992 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 998088011993 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 998088011994 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 998088011995 Predicted Na+/dicarboxylate symporter [General function prediction only]; Region: COG1823 998088011996 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 998088011997 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 998088011998 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 998088011999 YheO-like PAS domain; Region: PAS_6; pfam08348 998088012000 HTH domain; Region: HTH_22; pfam13309 998088012001 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088012002 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 998088012003 substrate binding pocket [chemical binding]; other site 998088012004 membrane-bound complex binding site; other site 998088012005 hinge residues; other site 998088012006 pyridine nucleotide transhydrogenase; Provisional; Region: pntB; PRK09444 998088012007 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 998088012008 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 998088012009 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 998088012010 ligand binding site [chemical binding]; other site 998088012011 homodimer interface [polypeptide binding]; other site 998088012012 NAD(P) binding site [chemical binding]; other site 998088012013 trimer interface B [polypeptide binding]; other site 998088012014 trimer interface A [polypeptide binding]; other site 998088012015 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 998088012016 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 998088012017 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 998088012018 dimer interface [polypeptide binding]; other site 998088012019 active site 998088012020 metal binding site [ion binding]; metal-binding site 998088012021 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 998088012022 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 998088012023 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 998088012024 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 998088012025 Cache domain; Region: Cache_1; pfam02743 998088012026 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 998088012027 dimerization interface [polypeptide binding]; other site 998088012028 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 998088012029 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088012030 dimer interface [polypeptide binding]; other site 998088012031 putative CheW interface [polypeptide binding]; other site 998088012032 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 998088012033 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; cd06587 998088012034 active site 998088012035 metal binding site [ion binding]; metal-binding site 998088012036 Transcriptional regulator [Transcription]; Region: LysR; COG0583 998088012037 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088012038 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 998088012039 dimerization interface [polypeptide binding]; other site 998088012040 Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism]; Region: PyrB; COG0540 998088012041 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 998088012042 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 998088012043 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 998088012044 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 998088012045 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 998088012046 putrescine transporter; Provisional; Region: potE; PRK10655 998088012047 ornithine decarboxylase; Provisional; Region: PRK13578 998088012048 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 998088012049 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 998088012050 homodimer interface [polypeptide binding]; other site 998088012051 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088012052 catalytic residue [active] 998088012053 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 998088012054 ornithine carbamoyltransferase; Validated; Region: PRK02102 998088012055 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 998088012056 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 998088012057 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 998088012058 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 998088012059 putative substrate binding site [chemical binding]; other site 998088012060 nucleotide binding site [chemical binding]; other site 998088012061 nucleotide binding site [chemical binding]; other site 998088012062 homodimer interface [polypeptide binding]; other site 998088012063 Amidinotransferase; Region: Amidinotransf; cl12043 998088012064 ParA-like protein; Provisional; Region: PHA02518 998088012065 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 998088012066 P-loop; other site 998088012067 Magnesium ion binding site [ion binding]; other site 998088012068 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 998088012069 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 998088012070 FeS/SAM binding site; other site 998088012071 HemN C-terminal domain; Region: HemN_C; pfam06969 998088012072 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 998088012073 Der GTPase activator (YihI); Region: YihI; pfam04220 998088012074 Cytochrome c553 [Energy production and conversion]; Region: COG2863 998088012075 Cytochrome c; Region: Cytochrom_C; cl11414 998088012076 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 998088012077 G1 box; other site 998088012078 GTP/Mg2+ binding site [chemical binding]; other site 998088012079 Switch I region; other site 998088012080 G2 box; other site 998088012081 G3 box; other site 998088012082 Switch II region; other site 998088012083 G4 box; other site 998088012084 G5 box; other site 998088012085 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 998088012086 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 998088012087 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 998088012088 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 998088012089 shikimate binding site; other site 998088012090 NAD(P) binding site [chemical binding]; other site 998088012091 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 998088012092 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 998088012093 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 998088012094 AIR carboxylase; Region: AIRC; pfam00731 998088012095 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 998088012096 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 998088012097 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 998088012098 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 998088012099 Protein of unknown function (DUF494); Region: DUF494; pfam04361 998088012100 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 998088012101 DNA protecting protein DprA; Region: dprA; TIGR00732 998088012102 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 998088012103 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 998088012104 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 998088012105 active site 998088012106 catalytic residues [active] 998088012107 metal binding site [ion binding]; metal-binding site 998088012108 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 998088012109 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 998088012110 putative active site [active] 998088012111 substrate binding site [chemical binding]; other site 998088012112 putative cosubstrate binding site; other site 998088012113 catalytic site [active] 998088012114 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 998088012115 substrate binding site [chemical binding]; other site 998088012116 16S rRNA methyltransferase B; Provisional; Region: PRK10901 998088012117 N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological...; Region: Methyltransferase_Sun; cd00620 998088012118 putative RNA binding site [nucleotide binding]; other site 998088012119 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 998088012120 S-adenosylmethionine binding site [chemical binding]; other site 998088012121 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 998088012122 TrkA-N domain; Region: TrkA_N; pfam02254 998088012123 TrkA-C domain; Region: TrkA_C; pfam02080 998088012124 TrkA-N domain; Region: TrkA_N; pfam02254 998088012125 TrkA-C domain; Region: TrkA_C; pfam02080 998088012126 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 998088012127 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 998088012128 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 998088012129 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 998088012130 G1 box; other site 998088012131 putative GEF interaction site [polypeptide binding]; other site 998088012132 GTP/Mg2+ binding site [chemical binding]; other site 998088012133 Switch I region; other site 998088012134 G2 box; other site 998088012135 G3 box; other site 998088012136 Switch II region; other site 998088012137 G4 box; other site 998088012138 G5 box; other site 998088012139 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 998088012140 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 998088012141 glutamine synthetase; Provisional; Region: glnA; PRK09469 998088012142 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 998088012143 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 998088012144 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 998088012145 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 998088012146 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 998088012147 putative active site [active] 998088012148 heme pocket [chemical binding]; other site 998088012149 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 998088012150 ATP binding site [chemical binding]; other site 998088012151 Mg2+ binding site [ion binding]; other site 998088012152 G-X-G motif; other site 998088012153 nitrogen regulation protein NR(I); Provisional; Region: glnG; PRK10923 998088012154 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 998088012155 active site 998088012156 phosphorylation site [posttranslational modification] 998088012157 intermolecular recognition site; other site 998088012158 dimerization interface [polypeptide binding]; other site 998088012159 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 998088012160 Walker A motif; other site 998088012161 ATP binding site [chemical binding]; other site 998088012162 Walker B motif; other site 998088012163 arginine finger; other site 998088012164 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 998088012165 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 998088012166 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 998088012167 active site 998088012168 purine riboside binding site [chemical binding]; other site 998088012169 RmuC family; Region: RmuC; pfam02646 998088012170 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 998088012171 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 998088012172 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 998088012173 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 998088012174 Predicted transcriptional regulator [Transcription]; Region: COG1959 998088012175 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088012176 DNA-binding site [nucleotide binding]; DNA binding site 998088012177 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 998088012178 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 998088012179 substrate binding site [chemical binding]; other site 998088012180 ATP binding site [chemical binding]; other site 998088012181 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 998088012182 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088012183 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 998088012184 dimerization interface [polypeptide binding]; other site 998088012185 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 998088012186 catalytic triad [active] 998088012187 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 998088012188 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 998088012189 tetrameric interface [polypeptide binding]; other site 998088012190 NAD binding site [chemical binding]; other site 998088012191 catalytic residues [active] 998088012192 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 998088012193 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 998088012194 inhibitor-cofactor binding pocket; inhibition site 998088012195 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088012196 catalytic residue [active] 998088012197 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 998088012198 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 998088012199 non-specific DNA binding site [nucleotide binding]; other site 998088012200 salt bridge; other site 998088012201 sequence-specific DNA binding site [nucleotide binding]; other site 998088012202 Cupin domain; Region: Cupin_2; pfam07883 998088012203 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 998088012204 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 998088012205 NAD(P) binding site [chemical binding]; other site 998088012206 catalytic residues [active] 998088012207 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 998088012208 EamA-like transporter family; Region: EamA; pfam00892 998088012209 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088012210 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088012211 dimer interface [polypeptide binding]; other site 998088012212 putative CheW interface [polypeptide binding]; other site 998088012213 Sulphur transport; Region: Sulf_transp; pfam04143 998088012214 outer membrane protein A; Reviewed; Region: PRK10808 998088012215 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 998088012216 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088012217 ligand binding site [chemical binding]; other site 998088012218 threonine dehydratase; Reviewed; Region: PRK09224 998088012219 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 998088012220 tetramer interface [polypeptide binding]; other site 998088012221 pyridoxal 5'-phosphate binding site [chemical binding]; other site 998088012222 catalytic residue [active] 998088012223 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 998088012224 putative Ile/Val binding site [chemical binding]; other site 998088012225 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 998088012226 putative Ile/Val binding site [chemical binding]; other site 998088012227 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 998088012228 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 998088012229 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 998088012230 homodimer interface [polypeptide binding]; other site 998088012231 substrate-cofactor binding pocket; other site 998088012232 catalytic residue [active] 998088012233 acetolactate synthase 2 regulatory subunit; Provisional; Region: ilvM; PRK11152 998088012234 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 998088012235 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 998088012236 PYR/PP interface [polypeptide binding]; other site 998088012237 dimer interface [polypeptide binding]; other site 998088012238 TPP binding site [chemical binding]; other site 998088012239 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 998088012240 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 998088012241 TPP-binding site [chemical binding]; other site 998088012242 dimer interface [polypeptide binding]; other site 998088012243 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 998088012244 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 998088012245 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 998088012246 Walker A motif; other site 998088012247 ATP binding site [chemical binding]; other site 998088012248 Walker B motif; other site 998088012249 arginine finger; other site 998088012250 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 998088012251 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 998088012252 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 998088012253 putative acyl-acceptor binding pocket; other site 998088012254 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 998088012255 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 998088012256 putative acyl-acceptor binding pocket; other site 998088012257 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 998088012258 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 998088012259 catalytic triad [active] 998088012260 metal binding site [ion binding]; metal-binding site 998088012261 conserved cis-peptide bond; other site 998088012262 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 998088012263 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 998088012264 active site 998088012265 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 998088012266 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 998088012267 catalytic residues [active] 998088012268 hinge region; other site 998088012269 alpha helical domain; other site 998088012270 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 998088012271 serine/threonine protein kinase; Provisional; Region: PRK11768 998088012272 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 998088012273 4Fe-4S binding domain; Region: Fer4_5; pfam12801 998088012274 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 998088012275 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 998088012276 Protein of unknown function (DUF1040); Region: DUF1040; pfam06288 998088012277 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088012278 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088012279 metal binding site [ion binding]; metal-binding site 998088012280 active site 998088012281 I-site; other site 998088012282 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 998088012283 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 998088012284 DNA binding residues [nucleotide binding] 998088012285 dimer interface [polypeptide binding]; other site 998088012286 copper binding site [ion binding]; other site 998088012287 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 998088012288 metal-binding site [ion binding] 998088012289 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 998088012290 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 998088012291 metal-binding site [ion binding] 998088012292 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 998088012293 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 998088012294 motif II; other site 998088012295 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 998088012296 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 998088012297 active site 998088012298 ribonuclease PH; Reviewed; Region: rph; PRK00173 998088012299 Ribonuclease PH; Region: RNase_PH_bact; cd11362 998088012300 hexamer interface [polypeptide binding]; other site 998088012301 active site 998088012302 hypothetical protein; Provisional; Region: PRK11820 998088012303 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 998088012304 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 998088012305 LysR family transcriptional regulator; Provisional; Region: PRK14997 998088012306 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088012307 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like_1; cd08470 998088012308 putative effector binding pocket; other site 998088012309 putative dimerization interface [polypeptide binding]; other site 998088012310 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 998088012311 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 998088012312 substrate binding site [chemical binding]; other site 998088012313 catalytic Zn binding site [ion binding]; other site 998088012314 NAD binding site [chemical binding]; other site 998088012315 structural Zn binding site [ion binding]; other site 998088012316 dimer interface [polypeptide binding]; other site 998088012317 S-formylglutathione hydrolase; Region: PLN02442 998088012318 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 998088012319 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 998088012320 5-histidylcysteine sulfoxide synthase; Region: ovoA_Nterm; TIGR04344 998088012321 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 998088012322 Methyltransferase domain; Region: Methyltransf_31; pfam13847 998088012323 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 998088012324 S-adenosylmethionine binding site [chemical binding]; other site 998088012325 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 998088012326 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 998088012327 inner membrane transporter YjeM; Provisional; Region: PRK15238 998088012328 tRNA-binding protein; Provisional; Region: PRK10089 998088012329 putative tRNA-binding site [nucleotide binding]; other site 998088012330 inner membrane transporter YjeM; Provisional; Region: PRK15238 998088012331 Domain of unknown function (DUF386); Region: DUF386; cl01047 998088012332 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 998088012333 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 998088012334 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 998088012335 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 998088012336 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 998088012337 DNA-binding transcriptional repressor EbgR; Provisional; Region: PRK10339 998088012338 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088012339 DNA binding site [nucleotide binding] 998088012340 domain linker motif; other site 998088012341 Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalR; cd01544 998088012342 putative dimerization interface [polypeptide binding]; other site 998088012343 putative ligand binding site [chemical binding]; other site 998088012344 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 998088012345 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 998088012346 trimer interface [polypeptide binding]; other site 998088012347 putative metal binding site [ion binding]; other site 998088012348 DNA polymerase I; Provisional; Region: PRK05755 998088012349 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 998088012350 active site 998088012351 metal binding site 1 [ion binding]; metal-binding site 998088012352 putative 5' ssDNA interaction site; other site 998088012353 metal binding site 3; metal-binding site 998088012354 metal binding site 2 [ion binding]; metal-binding site 998088012355 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 998088012356 putative DNA binding site [nucleotide binding]; other site 998088012357 putative metal binding site [ion binding]; other site 998088012358 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 998088012359 active site 998088012360 catalytic site [active] 998088012361 substrate binding site [chemical binding]; other site 998088012362 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 998088012363 active site 998088012364 DNA binding site [nucleotide binding] 998088012365 catalytic site [active] 998088012366 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 998088012367 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 998088012368 conserved cys residue [active] 998088012369 Protein of unknown function (DUF904); Region: DUF904; pfam06005 998088012370 serine acetyltransferase; Provisional; Region: cysE; PRK11132 998088012371 Serine acetyltransferase, N-terminal; Region: SATase_N; pfam06426 998088012372 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 998088012373 trimer interface [polypeptide binding]; other site 998088012374 active site 998088012375 substrate binding site [chemical binding]; other site 998088012376 CoA binding site [chemical binding]; other site 998088012377 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 998088012378 Cation efflux family; Region: Cation_efflux; cl00316 998088012379 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 998088012380 active site 998088012381 phosphorylation site [posttranslational modification] 998088012382 intermolecular recognition site; other site 998088012383 dimerization interface [polypeptide binding]; other site 998088012384 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 998088012385 DNA binding site [nucleotide binding] 998088012386 two-component sensor protein; Provisional; Region: cpxA; PRK09470 998088012387 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 998088012388 dimerization interface [polypeptide binding]; other site 998088012389 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 998088012390 dimer interface [polypeptide binding]; other site 998088012391 phosphorylation site [posttranslational modification] 998088012392 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 998088012393 ATP binding site [chemical binding]; other site 998088012394 Mg2+ binding site [ion binding]; other site 998088012395 G-X-G motif; other site 998088012396 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 998088012397 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 998088012398 putative efflux protein, MATE family; Region: matE; TIGR00797 998088012399 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 998088012400 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 998088012401 Cu(I) binding site [ion binding]; other site 998088012402 LexA repressor; Validated; Region: PRK00215 998088012403 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 998088012404 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 998088012405 Catalytic site [active] 998088012406 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 998088012407 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 998088012408 putative acyl-acceptor binding pocket; other site 998088012409 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 998088012410 UbiA prenyltransferase family; Region: UbiA; pfam01040 998088012411 Chorismate lyase; Region: Chor_lyase; cl01230 998088012412 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 998088012413 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 998088012414 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 998088012415 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 998088012416 NADP binding site [chemical binding]; other site 998088012417 dimer interface [polypeptide binding]; other site 998088012418 Transcriptional regulators [Transcription]; Region: PurR; COG1609 998088012419 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088012420 DNA binding site [nucleotide binding] 998088012421 domain linker motif; other site 998088012422 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 998088012423 putative dimerization interface [polypeptide binding]; other site 998088012424 putative ligand binding site [chemical binding]; other site 998088012425 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 998088012426 active site 998088012427 phosphorylation site [posttranslational modification] 998088012428 PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a...; Region: PTS_IIB_ascorbate; cd05563 998088012429 active site 998088012430 P-loop; other site 998088012431 phosphorylation site [posttranslational modification] 998088012432 PTS system ascorbate-specific transporter subunit IIC; Reviewed; Region: ulaA; PRK09410 998088012433 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 998088012434 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 998088012435 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 998088012436 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 998088012437 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 998088012438 putative active site [active] 998088012439 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 998088012440 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 998088012441 putative metal binding site; other site 998088012442 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 998088012443 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 998088012444 putative active site [active] 998088012445 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 998088012446 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 998088012447 active site 998088012448 (T/H)XGH motif; other site 998088012449 Protein of unknown function (DUF535); Region: DUF535; pfam04393 998088012450 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 998088012451 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 998088012452 DNA binding site [nucleotide binding] 998088012453 catalytic residue [active] 998088012454 H2TH interface [polypeptide binding]; other site 998088012455 putative catalytic residues [active] 998088012456 turnover-facilitating residue; other site 998088012457 intercalation triad [nucleotide binding]; other site 998088012458 8OG recognition residue [nucleotide binding]; other site 998088012459 putative reading head residues; other site 998088012460 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 998088012461 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 998088012462 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 998088012463 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 998088012464 hypothetical protein; Reviewed; Region: PRK00024 998088012465 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 998088012466 MPN+ (JAMM) motif; other site 998088012467 Zinc-binding site [ion binding]; other site 998088012468 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 998088012469 Flavoprotein; Region: Flavoprotein; pfam02441 998088012470 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 998088012471 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 998088012472 trimer interface [polypeptide binding]; other site 998088012473 active site 998088012474 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 998088012475 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 998088012476 active site 998088012477 DNA binding site [nucleotide binding] 998088012478 Int/Topo IB signature motif; other site 998088012479 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 998088012480 RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_II; cd03487 998088012481 putative active site [active] 998088012482 putative NTP binding site [chemical binding]; other site 998088012483 putative nucleic acid binding site [nucleotide binding]; other site 998088012484 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 998088012485 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 998088012486 Fic family protein [Function unknown]; Region: COG3177 998088012487 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 998088012488 Fic/DOC family; Region: Fic; pfam02661 998088012489 CRISPR/Cas system-associated transcriptional regulator CasRa; Region: CasRa_I-A; cd09655 998088012490 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 998088012491 RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_I; cd01646 998088012492 putative active site [active] 998088012493 putative NTP binding site [chemical binding]; other site 998088012494 putative nucleic acid binding site [nucleotide binding]; other site 998088012495 Tetratricopeptide repeat; Region: TPR_15; pfam13429 998088012496 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 998088012497 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 998088012498 active site 998088012499 division inhibitor protein; Provisional; Region: slmA; PRK09480 998088012500 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 998088012501 mechanosensitive channel MscS; Provisional; Region: PRK10334 998088012502 Conserved TM helix; Region: TM_helix; pfam05552 998088012503 Mechanosensitive ion channel; Region: MS_channel; pfam00924 998088012504 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 998088012505 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 998088012506 active site 998088012507 dimer interface [polypeptide binding]; other site 998088012508 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 998088012509 dimer interface [polypeptide binding]; other site 998088012510 active site 998088012511 ketol-acid reductoisomerase; Validated; Region: PRK05225 998088012512 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 998088012513 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 998088012514 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 998088012515 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 998088012516 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 998088012517 The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; Region: PBP2_IlvY; cd08430 998088012518 putative dimerization interface [polypeptide binding]; other site 998088012519 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088012520 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 998088012521 CoA binding domain; Region: CoA_binding_2; pfam13380 998088012522 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 998088012523 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 998088012524 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 998088012525 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 998088012526 Flavodoxin domain; Region: Flavodoxin_5; cl17428 998088012527 Cation transport protein; Region: TrkH; cl17365 998088012528 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 998088012529 hypothetical protein; Provisional; Region: PRK11568 998088012530 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 998088012531 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 998088012532 proline dipeptidase; Provisional; Region: PRK13607 998088012533 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 998088012534 active site 998088012535 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 998088012536 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 998088012537 acyl-activating enzyme (AAE) consensus motif; other site 998088012538 putative AMP binding site [chemical binding]; other site 998088012539 putative active site [active] 998088012540 putative CoA binding site [chemical binding]; other site 998088012541 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 998088012542 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 998088012543 substrate binding site [chemical binding]; other site 998088012544 oxyanion hole (OAH) forming residues; other site 998088012545 trimer interface [polypeptide binding]; other site 998088012546 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 998088012547 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 998088012548 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 998088012549 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 998088012550 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 998088012551 dimer interface [polypeptide binding]; other site 998088012552 active site 998088012553 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 998088012554 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 998088012555 active site 998088012556 phosphorylation site [posttranslational modification] 998088012557 intermolecular recognition site; other site 998088012558 dimerization interface [polypeptide binding]; other site 998088012559 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 998088012560 DNA binding site [nucleotide binding] 998088012561 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 998088012562 dimerization interface [polypeptide binding]; other site 998088012563 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 998088012564 ATP binding site [chemical binding]; other site 998088012565 Mg2+ binding site [ion binding]; other site 998088012566 G-X-G motif; other site 998088012567 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 998088012568 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 998088012569 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 998088012570 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_2; cd06150 998088012571 homotrimer interaction site [polypeptide binding]; other site 998088012572 putative active site [active] 998088012573 putative outer membrane lipoprotein; Provisional; Region: PRK10510 998088012574 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 998088012575 ligand binding site [chemical binding]; other site 998088012576 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 998088012577 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 998088012578 dimer interface [polypeptide binding]; other site 998088012579 motif 1; other site 998088012580 active site 998088012581 motif 2; other site 998088012582 motif 3; other site 998088012583 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 998088012584 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 998088012585 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 998088012586 Electron transfer DM13; Region: DM13; pfam10517 998088012587 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 998088012588 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 998088012589 dimerization interface [polypeptide binding]; other site 998088012590 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 998088012591 dimer interface [polypeptide binding]; other site 998088012592 putative CheW interface [polypeptide binding]; other site 998088012593 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 998088012594 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 998088012595 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 998088012596 DNA-binding site [nucleotide binding]; DNA binding site 998088012597 UTRA domain; Region: UTRA; pfam07702 998088012598 PTS system, alpha-glucoside-specific IIBC component; Region: PTS-IIBC-alpha; TIGR02005 998088012599 PTS system, maltose and glucose-specific subfamily, IIC component; Region: pts-Glc; TIGR00852 998088012600 PTS_IIB, PTS system, glucose/sucrose specific IIB 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_IIB_glc; cd00212 998088012601 active site turn [active] 998088012602 phosphorylation site [posttranslational modification] 998088012603 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 998088012604 Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases; Region: GH4_GlvA_pagL_like; cd05298 998088012605 NAD binding site [chemical binding]; other site 998088012606 sugar binding site [chemical binding]; other site 998088012607 divalent metal binding site [ion binding]; other site 998088012608 putative tetramer (dimer of dimers) interface [polypeptide binding]; other site 998088012609 dimer interface [polypeptide binding]; other site 998088012610 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 998088012611 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 998088012612 DNA binding site [nucleotide binding] 998088012613 domain linker motif; other site 998088012614 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 998088012615 dimerization interface [polypeptide binding]; other site 998088012616 ligand binding site [chemical binding]; other site 998088012617 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 998088012618 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 998088012619 dimerization interface [polypeptide binding]; other site 998088012620 ligand binding site [chemical binding]; other site 998088012621 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 998088012622 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 998088012623 TM-ABC transporter signature motif; other site 998088012624 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 998088012625 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 998088012626 TM-ABC transporter signature motif; other site 998088012627 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 998088012628 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 998088012629 Walker A/P-loop; other site 998088012630 ATP binding site [chemical binding]; other site 998088012631 Q-loop/lid; other site 998088012632 ABC transporter signature motif; other site 998088012633 Walker B; other site 998088012634 D-loop; other site 998088012635 H-loop/switch region; other site 998088012636 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livF; PRK11614 998088012637 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 998088012638 Walker A/P-loop; other site 998088012639 ATP binding site [chemical binding]; other site 998088012640 Q-loop/lid; other site 998088012641 ABC transporter signature motif; other site 998088012642 Walker B; other site 998088012643 D-loop; other site 998088012644 H-loop/switch region; other site 998088012645 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 998088012646 active site residue [active] 998088012647 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 998088012648 rhomboid family protease GlpG; Region: rhombo_GlpG; TIGR04239 998088012649 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 998088012650 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 998088012651 Bacterial virulence factor lipase N-terminal; Region: Lipase_bact_N; pfam12262 998088012652 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2960 998088012653 PAS fold; Region: PAS_3; pfam08447 998088012654 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088012655 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088012656 metal binding site [ion binding]; metal-binding site 998088012657 active site 998088012658 I-site; other site 998088012659 FMN reductase; Validated; Region: fre; PRK08051 998088012660 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 998088012661 FAD binding pocket [chemical binding]; other site 998088012662 FAD binding motif [chemical binding]; other site 998088012663 phosphate binding motif [ion binding]; other site 998088012664 beta-alpha-beta structure motif; other site 998088012665 NAD binding pocket [chemical binding]; other site 998088012666 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 998088012667 transcription termination factor Rho; Provisional; Region: rho; PRK09376 998088012668 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 998088012669 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 998088012670 RNA binding site [nucleotide binding]; other site 998088012671 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 998088012672 multimer interface [polypeptide binding]; other site 998088012673 Walker A motif; other site 998088012674 ATP binding site [chemical binding]; other site 998088012675 Walker B motif; other site 998088012676 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 998088012677 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 998088012678 catalytic residues [active] 998088012679 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 998088012680 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 998088012681 ATP binding site [chemical binding]; other site 998088012682 Mg++ binding site [ion binding]; other site 998088012683 motif III; other site 998088012684 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 998088012685 nucleotide binding region [chemical binding]; other site 998088012686 ATP-binding site [chemical binding]; other site 998088012687 guanosine pentaphosphate phosphohydrolase; Provisional; Region: PRK11031 998088012688 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 998088012689 nucleotide binding site [chemical binding]; other site 998088012690 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; cl09210 998088012691 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 998088012692 S-adenosylmethionine binding site [chemical binding]; other site 998088012693 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 998088012694 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088012695 substrate binding pocket [chemical binding]; other site 998088012696 membrane-bound complex binding site; other site 998088012697 hinge residues; other site 998088012698 PAS domain S-box; Region: sensory_box; TIGR00229 998088012699 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 998088012700 putative active site [active] 998088012701 heme pocket [chemical binding]; other site 998088012702 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 998088012703 PAS domain; Region: PAS_9; pfam13426 998088012704 putative active site [active] 998088012705 heme pocket [chemical binding]; other site 998088012706 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 998088012707 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 998088012708 metal binding site [ion binding]; metal-binding site 998088012709 active site 998088012710 I-site; other site 998088012711 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 998088012712 oligopeptidase A; Provisional; Region: PRK10911 998088012713 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 998088012714 active site 998088012715 Zn binding site [ion binding]; other site 998088012716 Glycosyl hydrolases family 18; Region: Glyco_hydro_18; pfam00704 998088012717 GH18 domain of Chitinase D (ChiD). ChiD, a chitinase found in Bacillus circulans, hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine in chitin and chitodextrins. The domain architecture of ChiD includes a catalytic glycosyl hydrolase family 18; Region: GH18_chitinase_D-like; cd02871 998088012718 putative active site [active] 998088012719 Bacterial Ig-like domain (group 3); Region: Big_3; pfam07523 998088012720 Bacterial Ig-like domain (group 3); Region: Big_3; pfam07523 998088012721 Chitin-binding domain of chitinase C; Region: ChiC_BD; cd12215 998088012722 aromatic chitin/cellulose binding site residues [chemical binding]; other site 998088012723 chitin-binding domain of Chi A1-like proteins; Region: ChiA1_BD; cd12214 998088012724 ToxR activated gene A lipoprotein; Region: TagA; pfam12561 998088012725 chitin-binding domain of Chi A1-like proteins; Region: ChiA1_BD; cd12214 998088012726 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 998088012727 dimer interface [polypeptide binding]; other site 998088012728 allosteric magnesium binding site [ion binding]; other site 998088012729 active site 998088012730 aspartate-rich active site metal binding site; other site 998088012731 Schiff base residues; other site 998088012732 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 998088012733 active site 998088012734 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 998088012735 sec-independent translocase; Provisional; Region: PRK01770 998088012736 sec-independent translocase; Provisional; Region: tatB; PRK00404 998088012737 twin arginine translocase protein A; Provisional; Region: tatA; PRK04598 998088012738 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 998088012739 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 998088012740 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 998088012741 SCP-2 sterol transfer family; Region: SCP2; pfam02036 998088012742 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 998088012743 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 998088012744 S-adenosylmethionine binding site [chemical binding]; other site 998088012745 CrcB-like protein; Region: CRCB; cl09114 998088012746 cytosine deaminase; Provisional; Region: PRK09230 998088012747 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 998088012748 active site 998088012749 nucleobase-cation-symport-1 (NCS1) transporter CobB-like; solute-binding domain; Region: SLC-NCS1sbd_CobB-like; cd11484 998088012750 Na binding site [ion binding]; other site 998088012751 putative substrate binding site [chemical binding]; other site 998088012752 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 998088012753 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 998088012754 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 998088012755 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 998088012756 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 998088012757 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 998088012758 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 998088012759 Autoinducer binding domain; Region: Autoind_bind; pfam03472 998088012760 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 998088012761 DNA binding residues [nucleotide binding] 998088012762 dimerization interface [polypeptide binding]; other site 998088012763 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 998088012764 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 998088012765 glutaminase active site [active] 998088012766 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 998088012767 dimer interface [polypeptide binding]; other site 998088012768 active site 998088012769 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 998088012770 dimer interface [polypeptide binding]; other site 998088012771 active site 998088012772 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 998088012773 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 998088012774 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 998088012775 DNA-binding response regulator CreB; Provisional; Region: PRK11083 998088012776 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 998088012777 active site 998088012778 phosphorylation site [posttranslational modification] 998088012779 intermolecular recognition site; other site 998088012780 dimerization interface [polypeptide binding]; other site 998088012781 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 998088012782 DNA binding site [nucleotide binding] 998088012783 sensory histidine kinase CreC; Provisional; Region: PRK11100 998088012784 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 998088012785 dimer interface [polypeptide binding]; other site 998088012786 phosphorylation site [posttranslational modification] 998088012787 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 998088012788 ATP binding site [chemical binding]; other site 998088012789 Mg2+ binding site [ion binding]; other site 998088012790 G-X-G motif; other site 998088012791 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 998088012792 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 998088012793 inner membrane protein; Provisional; Region: PRK11715 998088012794 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 998088012795 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 998088012796 Substrate binding site; other site 998088012797 Mg++ binding site; other site 998088012798 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 998088012799 active site 998088012800 substrate binding site [chemical binding]; other site 998088012801 CoA binding site [chemical binding]; other site 998088012802 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 998088012803 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 998088012804 gamma subunit interface [polypeptide binding]; other site 998088012805 epsilon subunit interface [polypeptide binding]; other site 998088012806 LBP interface [polypeptide binding]; other site 998088012807 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 998088012808 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 998088012809 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 998088012810 alpha subunit interaction interface [polypeptide binding]; other site 998088012811 Walker A motif; other site 998088012812 ATP binding site [chemical binding]; other site 998088012813 Walker B motif; other site 998088012814 inhibitor binding site; inhibition site 998088012815 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 998088012816 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 998088012817 core domain interface [polypeptide binding]; other site 998088012818 delta subunit interface [polypeptide binding]; other site 998088012819 epsilon subunit interface [polypeptide binding]; other site 998088012820 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 998088012821 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 998088012822 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 998088012823 beta subunit interaction interface [polypeptide binding]; other site 998088012824 Walker A motif; other site 998088012825 ATP binding site [chemical binding]; other site 998088012826 Walker B motif; other site 998088012827 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 998088012828 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 998088012829 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 998088012830 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 998088012831 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 998088012832 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 998088012833 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 998088012834 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 998088012835 ATP synthase I chain; Region: ATP_synt_I; cl09170 998088012836 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 998088012837 ParB-like nuclease domain; Region: ParB; smart00470 998088012838 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 998088012839 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 998088012840 P loop; other site 998088012841 Nucleotide binding site [chemical binding]; other site 998088012842 DTAP/Switch II; other site 998088012843 Switch I; other site 998088012844 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 998088012845 Magnesium ion binding site [ion binding]; other site 998088012846 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 998088012847 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 998088012848 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 998088012849 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 998088012850 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 998088012851 FMN-binding protein MioC; Provisional; Region: PRK09004 998088012852 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 998088012853 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 998088012854 N-terminal plug; other site 998088012855 ligand-binding site [chemical binding]; other site 998088012856 multidrug transporter membrane component/ATP-binding component; Provisional; Region: PRK10522 998088012857 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 998088012858 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 998088012859 Walker A/P-loop; other site 998088012860 ATP binding site [chemical binding]; other site 998088012861 Q-loop/lid; other site 998088012862 ABC transporter signature motif; other site 998088012863 Walker B; other site 998088012864 D-loop; other site 998088012865 H-loop/switch region; other site 998088012866 iron-hydroxamate transporter ATP-binding subunit; Provisional; Region: PRK10575 998088012867 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 998088012868 Walker A/P-loop; other site 998088012869 ATP binding site [chemical binding]; other site 998088012870 Q-loop/lid; other site 998088012871 ABC transporter signature motif; other site 998088012872 Walker B; other site 998088012873 D-loop; other site 998088012874 H-loop/switch region; other site 998088012875 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 998088012876 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 998088012877 siderophore binding site; other site 998088012878 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 998088012879 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 998088012880 ABC-ATPase subunit interface; other site 998088012881 dimer interface [polypeptide binding]; other site 998088012882 putative PBP binding regions; other site 998088012883 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 998088012884 ABC-ATPase subunit interface; other site 998088012885 dimer interface [polypeptide binding]; other site 998088012886 putative PBP binding regions; other site 998088012887 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 998088012888 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 998088012889 trmE is a tRNA modification GTPase; Region: trmE; cd04164 998088012890 G1 box; other site 998088012891 GTP/Mg2+ binding site [chemical binding]; other site 998088012892 Switch I region; other site 998088012893 G2 box; other site 998088012894 Switch II region; other site 998088012895 G3 box; other site 998088012896 G4 box; other site 998088012897 G5 box; other site 998088012898 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 998088012899 membrane protein insertase; Provisional; Region: PRK01318 998088012900 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 998088012901 Ribonuclease P; Region: Ribonuclease_P; cl00457 998088012902 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 998088012903 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 998088012904 Walker A/P-loop; other site 998088012905 ATP binding site [chemical binding]; other site 998088012906 Q-loop/lid; other site 998088012907 ABC transporter signature motif; other site 998088012908 Walker B; other site 998088012909 D-loop; other site 998088012910 H-loop/switch region; other site 998088012911 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 998088012912 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 998088012913 dimer interface [polypeptide binding]; other site 998088012914 conserved gate region; other site 998088012915 putative PBP binding loops; other site 998088012916 ABC-ATPase subunit interface; other site 998088012917 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 998088012918 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 998088012919 substrate binding pocket [chemical binding]; other site 998088012920 membrane-bound complex binding site; other site 998088012921 hinge residues; other site