-- dump date 20140620_064407 -- class Genbank::misc_feature -- table misc_feature_note -- id note 399804000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 399804000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 399804000003 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 399804000004 Walker A motif; other site 399804000005 ATP binding site [chemical binding]; other site 399804000006 Walker B motif; other site 399804000007 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 399804000008 arginine finger; other site 399804000009 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 399804000010 DnaA box-binding interface [nucleotide binding]; other site 399804000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 399804000012 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 399804000013 putative DNA binding surface [nucleotide binding]; other site 399804000014 dimer interface [polypeptide binding]; other site 399804000015 beta-clamp/clamp loader binding surface; other site 399804000016 beta-clamp/translesion DNA polymerase binding surface; other site 399804000017 recombination protein F; Reviewed; Region: recF; PRK00064 399804000018 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804000019 Walker A/P-loop; other site 399804000020 ATP binding site [chemical binding]; other site 399804000021 Q-loop/lid; other site 399804000022 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804000023 ABC transporter signature motif; other site 399804000024 Walker B; other site 399804000025 D-loop; other site 399804000026 H-loop/switch region; other site 399804000027 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 399804000028 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 399804000029 ATP binding site [chemical binding]; other site 399804000030 Mg2+ binding site [ion binding]; other site 399804000031 G-X-G motif; other site 399804000032 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 399804000033 anchoring element; other site 399804000034 dimer interface [polypeptide binding]; other site 399804000035 ATP binding site [chemical binding]; other site 399804000036 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 399804000037 active site 399804000038 putative metal-binding site [ion binding]; other site 399804000039 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 399804000040 HDOD domain; Region: HDOD; pfam08668 399804000041 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804000042 Zn2+ binding site [ion binding]; other site 399804000043 Mg2+ binding site [ion binding]; other site 399804000044 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 399804000045 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 399804000046 dimer interface [polypeptide binding]; other site 399804000047 motif 1; other site 399804000048 active site 399804000049 motif 2; other site 399804000050 motif 3; other site 399804000051 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 399804000052 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804000053 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 399804000054 Amidohydrolase; Region: Amidohydro_5; pfam13594 399804000055 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cd01292 399804000056 active site 399804000057 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 399804000058 MOSC domain; Region: MOSC; pfam03473 399804000059 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 399804000060 CPxP motif; other site 399804000061 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 399804000062 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 399804000063 dimer interface [polypeptide binding]; other site 399804000064 active site 399804000065 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 399804000066 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 399804000067 substrate binding site [chemical binding]; other site 399804000068 oxyanion hole (OAH) forming residues; other site 399804000069 trimer interface [polypeptide binding]; other site 399804000070 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 399804000071 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 399804000072 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 399804000073 proline dipeptidase; Provisional; Region: PRK13607 399804000074 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 399804000075 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 399804000076 active site 399804000077 hypothetical protein; Provisional; Region: PRK11568 399804000078 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 399804000079 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 399804000080 Cation transport protein; Region: TrkH; cl17365 399804000081 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 399804000082 Flavodoxin domain; Region: Flavodoxin_5; cl17428 399804000083 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 399804000084 dimerization interface [polypeptide binding]; other site 399804000085 putative DNA binding site [nucleotide binding]; other site 399804000086 putative Zn2+ binding site [ion binding]; other site 399804000087 Flavodoxin domain; Region: Flavodoxin_5; cl17428 399804000088 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 399804000089 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 399804000090 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 399804000091 TrkA-N domain; Region: TrkA_N; pfam02254 399804000092 TrkA-C domain; Region: TrkA_C; pfam02080 399804000093 TrkA-N domain; Region: TrkA_N; pfam02254 399804000094 TrkA-C domain; Region: TrkA_C; pfam02080 399804000095 16S rRNA methyltransferase B; Provisional; Region: PRK10901 399804000096 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 399804000097 putative RNA binding site [nucleotide binding]; other site 399804000098 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 399804000099 S-adenosylmethionine binding site [chemical binding]; other site 399804000100 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 399804000101 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 399804000102 putative active site [active] 399804000103 substrate binding site [chemical binding]; other site 399804000104 putative cosubstrate binding site; other site 399804000105 catalytic site [active] 399804000106 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 399804000107 substrate binding site [chemical binding]; other site 399804000108 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 399804000109 active site 399804000110 catalytic residues [active] 399804000111 metal binding site [ion binding]; metal-binding site 399804000112 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804000113 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 399804000114 DNA protecting protein DprA; Region: dprA; TIGR00732 399804000115 Protein of unknown function (DUF494); Region: DUF494; pfam04361 399804000116 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 399804000117 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 399804000118 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 399804000119 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 399804000120 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 399804000121 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 399804000122 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 399804000123 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 399804000124 apolar tunnel; other site 399804000125 heme binding site [chemical binding]; other site 399804000126 dimerization interface [polypeptide binding]; other site 399804000127 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 399804000128 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 399804000129 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 399804000130 shikimate binding site; other site 399804000131 NAD(P) binding site [chemical binding]; other site 399804000132 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 399804000133 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 399804000134 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 399804000135 trimer interface [polypeptide binding]; other site 399804000136 putative metal binding site [ion binding]; other site 399804000137 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 399804000138 PAS fold; Region: PAS_3; pfam08447 399804000139 putative active site [active] 399804000140 heme pocket [chemical binding]; other site 399804000141 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804000142 metal binding site [ion binding]; metal-binding site 399804000143 active site 399804000144 I-site; other site 399804000145 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 399804000146 lysophospholipase L2; Provisional; Region: PRK10749 399804000147 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 399804000148 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 399804000149 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 399804000150 adenosine deaminase; Provisional; Region: PRK09358 399804000151 active site 399804000152 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 399804000153 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 399804000154 FeS/SAM binding site; other site 399804000155 HemN C-terminal domain; Region: HemN_C; pfam06969 399804000156 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 399804000157 Der GTPase activator (YihI); Region: YihI; pfam04220 399804000158 Methyltransferase domain; Region: Methyltransf_23; pfam13489 399804000159 Cytochrome c553 [Energy production and conversion]; Region: COG2863 399804000160 Cytochrome c; Region: Cytochrom_C; cl11414 399804000161 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 399804000162 G1 box; other site 399804000163 GTP/Mg2+ binding site [chemical binding]; other site 399804000164 Switch I region; other site 399804000165 G2 box; other site 399804000166 G3 box; other site 399804000167 Switch II region; other site 399804000168 G4 box; other site 399804000169 G5 box; other site 399804000170 DNA polymerase I; Provisional; Region: PRK05755 399804000171 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 399804000172 active site 399804000173 metal binding site 1 [ion binding]; metal-binding site 399804000174 putative 5' ssDNA interaction site; other site 399804000175 metal binding site 3; metal-binding site 399804000176 metal binding site 2 [ion binding]; metal-binding site 399804000177 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 399804000178 putative DNA binding site [nucleotide binding]; other site 399804000179 putative metal binding site [ion binding]; other site 399804000180 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 399804000181 active site 399804000182 catalytic site [active] 399804000183 substrate binding site [chemical binding]; other site 399804000184 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 399804000185 active site 399804000186 DNA binding site [nucleotide binding] 399804000187 catalytic site [active] 399804000188 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 399804000189 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 399804000190 conserved cys residue [active] 399804000191 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 399804000192 rhomboid family protease GlpG; Region: rhombo_GlpG; TIGR04239 399804000193 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 399804000194 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 399804000195 active site residue [active] 399804000196 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 399804000197 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 399804000198 NAD(P) binding site [chemical binding]; other site 399804000199 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 399804000200 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 399804000201 substrate-cofactor binding pocket; other site 399804000202 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804000203 catalytic residue [active] 399804000204 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804000205 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804000206 Bacterial transcriptional repressor; Region: TetR; pfam13972 399804000207 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 399804000208 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 399804000209 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 399804000210 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; pfam06293 399804000211 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 399804000212 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 399804000213 putative active site [active] 399804000214 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 399804000215 active site 399804000216 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 399804000217 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 399804000218 NAD binding site [chemical binding]; other site 399804000219 substrate binding site [chemical binding]; other site 399804000220 homodimer interface [polypeptide binding]; other site 399804000221 active site 399804000222 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 399804000223 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 399804000224 substrate binding site; other site 399804000225 tetramer interface; other site 399804000226 WxcM-like, C-terminal; Region: FdtA; pfam05523 399804000227 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 399804000228 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 399804000229 putative trimer interface [polypeptide binding]; other site 399804000230 putative active site [active] 399804000231 putative substrate binding site [chemical binding]; other site 399804000232 putative CoA binding site [chemical binding]; other site 399804000233 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 399804000234 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 399804000235 inhibitor-cofactor binding pocket; inhibition site 399804000236 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804000237 catalytic residue [active] 399804000238 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 399804000239 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 399804000240 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 399804000241 putative metal binding site; other site 399804000242 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 399804000243 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 399804000244 NADP binding site [chemical binding]; other site 399804000245 active site 399804000246 putative substrate binding site [chemical binding]; other site 399804000247 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 399804000248 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 399804000249 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 399804000250 Sulfatase; Region: Sulfatase; pfam00884 399804000251 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 399804000252 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 399804000253 active site 399804000254 (T/H)XGH motif; other site 399804000255 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 399804000256 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 399804000257 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 399804000258 DNA binding site [nucleotide binding] 399804000259 catalytic residue [active] 399804000260 H2TH interface [polypeptide binding]; other site 399804000261 putative catalytic residues [active] 399804000262 turnover-facilitating residue; other site 399804000263 intercalation triad [nucleotide binding]; other site 399804000264 8OG recognition residue [nucleotide binding]; other site 399804000265 putative reading head residues; other site 399804000266 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 399804000267 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 399804000268 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 399804000269 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 399804000270 FeS/SAM binding site; other site 399804000271 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 399804000272 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional; Region: PRK14491 399804000273 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 399804000274 Walker A motif; other site 399804000275 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 399804000276 dimer interface [polypeptide binding]; other site 399804000277 putative functional site; other site 399804000278 putative MPT binding site; other site 399804000279 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 399804000280 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 399804000281 GTP binding site; other site 399804000282 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 399804000283 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 399804000284 Walker A/P-loop; other site 399804000285 ATP binding site [chemical binding]; other site 399804000286 Q-loop/lid; other site 399804000287 ABC transporter signature motif; other site 399804000288 Walker B; other site 399804000289 D-loop; other site 399804000290 H-loop/switch region; other site 399804000291 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 399804000292 dimer interface [polypeptide binding]; other site 399804000293 conserved gate region; other site 399804000294 putative PBP binding loops; other site 399804000295 ABC-ATPase subunit interface; other site 399804000296 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 399804000297 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 399804000298 dimerization interface [polypeptide binding]; other site 399804000299 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 399804000300 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 399804000301 active site 399804000302 phosphorylation site [posttranslational modification] 399804000303 intermolecular recognition site; other site 399804000304 dimerization interface [polypeptide binding]; other site 399804000305 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 399804000306 Walker A motif; other site 399804000307 ATP binding site [chemical binding]; other site 399804000308 Walker B motif; other site 399804000309 arginine finger; other site 399804000310 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804000311 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804000312 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 399804000313 dimer interface [polypeptide binding]; other site 399804000314 phosphorylation site [posttranslational modification] 399804000315 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 399804000316 ATP binding site [chemical binding]; other site 399804000317 G-X-G motif; other site 399804000318 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804000319 Coenzyme A binding pocket [chemical binding]; other site 399804000320 hypothetical protein; Provisional; Region: PRK11212 399804000321 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 399804000322 chorismate binding enzyme; Region: Chorismate_bind; cl10555 399804000323 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 399804000324 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 399804000325 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 399804000326 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 399804000327 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 399804000328 Walker A/P-loop; other site 399804000329 ATP binding site [chemical binding]; other site 399804000330 Q-loop/lid; other site 399804000331 ABC transporter signature motif; other site 399804000332 Walker B; other site 399804000333 D-loop; other site 399804000334 H-loop/switch region; other site 399804000335 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 399804000336 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 399804000337 Walker A/P-loop; other site 399804000338 ATP binding site [chemical binding]; other site 399804000339 Q-loop/lid; other site 399804000340 ABC transporter signature motif; other site 399804000341 Walker B; other site 399804000342 D-loop; other site 399804000343 H-loop/switch region; other site 399804000344 Cobalt transport protein; Region: CbiQ; cl00463 399804000345 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 399804000346 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 399804000347 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804000348 Zn2+ binding site [ion binding]; other site 399804000349 Mg2+ binding site [ion binding]; other site 399804000350 Paraquat-inducible protein A; Region: PqiA; pfam04403 399804000351 Predicted membrane protein [Function unknown]; Region: COG2855 399804000352 malate synthase; Provisional; Region: PRK08951 399804000353 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 399804000354 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 399804000355 non-specific DNA binding site [nucleotide binding]; other site 399804000356 salt bridge; other site 399804000357 sequence-specific DNA binding site [nucleotide binding]; other site 399804000358 Domain of unknown function (DUF955); Region: DUF955; cl01076 399804000359 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 399804000360 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; COG2040 399804000361 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 399804000362 transporter, basic amino acid/polyamine antiporter (APA) family; Region: 2A0302; TIGR00905 399804000363 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 399804000364 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 399804000365 N-terminal plug; other site 399804000366 ligand-binding site [chemical binding]; other site 399804000367 protoheme IX farnesyltransferase; Provisional; Region: PRK13362 399804000368 UbiA prenyltransferase family; Region: UbiA; pfam01040 399804000369 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 399804000370 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 399804000371 Subunit I/III interface [polypeptide binding]; other site 399804000372 Subunit III/IV interface [polypeptide binding]; other site 399804000373 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 399804000374 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 399804000375 D-pathway; other site 399804000376 Putative ubiquinol binding site [chemical binding]; other site 399804000377 Low-spin heme (heme b) binding site [chemical binding]; other site 399804000378 Putative water exit pathway; other site 399804000379 Binuclear center (heme o3/CuB) [ion binding]; other site 399804000380 K-pathway; other site 399804000381 Putative proton exit pathway; other site 399804000382 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 399804000383 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 399804000384 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 399804000385 Homeodomain-like domain; Region: HTH_23; pfam13384 399804000386 Winged helix-turn helix; Region: HTH_29; pfam13551 399804000387 Winged helix-turn helix; Region: HTH_33; pfam13592 399804000388 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804000389 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804000390 Protein of unknown function (DUF3300); Region: DUF3300; pfam11737 399804000391 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 399804000392 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 399804000393 ATP binding site [chemical binding]; other site 399804000394 Mg2+ binding site [ion binding]; other site 399804000395 G-X-G motif; other site 399804000396 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804000397 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 399804000398 active site 399804000399 phosphorylation site [posttranslational modification] 399804000400 intermolecular recognition site; other site 399804000401 dimerization interface [polypeptide binding]; other site 399804000402 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 399804000403 DNA binding site [nucleotide binding] 399804000404 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 399804000405 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 399804000406 catalytic triad [active] 399804000407 dimer interface [polypeptide binding]; other site 399804000408 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804000409 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 399804000410 dimerization interface [polypeptide binding]; other site 399804000411 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804000412 dimer interface [polypeptide binding]; other site 399804000413 putative CheW interface [polypeptide binding]; other site 399804000414 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 399804000415 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 399804000416 dimerization interface [polypeptide binding]; other site 399804000417 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 399804000418 dimer interface [polypeptide binding]; other site 399804000419 phosphorylation site [posttranslational modification] 399804000420 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 399804000421 ATP binding site [chemical binding]; other site 399804000422 Mg2+ binding site [ion binding]; other site 399804000423 G-X-G motif; other site 399804000424 osmolarity response regulator; Provisional; Region: ompR; PRK09468 399804000425 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 399804000426 active site 399804000427 phosphorylation site [posttranslational modification] 399804000428 intermolecular recognition site; other site 399804000429 dimerization interface [polypeptide binding]; other site 399804000430 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 399804000431 DNA binding site [nucleotide binding] 399804000432 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 399804000433 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 399804000434 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 399804000435 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 399804000436 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 399804000437 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 399804000438 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 399804000439 RNA binding site [nucleotide binding]; other site 399804000440 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 399804000441 Sulfatase; Region: Sulfatase; pfam00884 399804000442 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 399804000443 DNA utilization protein GntX; Provisional; Region: PRK11595 399804000444 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 399804000445 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 399804000446 dimerization interface [polypeptide binding]; other site 399804000447 DNA binding residues [nucleotide binding] 399804000448 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804000449 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 399804000450 active site 399804000451 phosphorylation site [posttranslational modification] 399804000452 intermolecular recognition site; other site 399804000453 dimerization interface [polypeptide binding]; other site 399804000454 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 399804000455 DNA binding site [nucleotide binding] 399804000456 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804000457 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 399804000458 dimer interface [polypeptide binding]; other site 399804000459 phosphorylation site [posttranslational modification] 399804000460 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 399804000461 ATP binding site [chemical binding]; other site 399804000462 Mg2+ binding site [ion binding]; other site 399804000463 G-X-G motif; other site 399804000464 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 399804000465 FMN-binding domain; Region: FMN_bind; pfam04205 399804000466 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 399804000467 L-aspartate oxidase; Provisional; Region: PRK06175 399804000468 Predicted oxidoreductase [General function prediction only]; Region: COG3573 399804000469 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 399804000470 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 399804000471 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 399804000472 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 399804000473 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 399804000474 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u4_5s; cd10973 399804000475 putative active site [active] 399804000476 putative metal binding site [ion binding]; other site 399804000477 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 399804000478 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 399804000479 Cu(I) binding site [ion binding]; other site 399804000480 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 399804000481 UbiA prenyltransferase family; Region: UbiA; pfam01040 399804000482 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 399804000483 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 399804000484 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 399804000485 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 399804000486 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 399804000487 Subunit III/VIIa interface [polypeptide binding]; other site 399804000488 Phospholipid binding site [chemical binding]; other site 399804000489 Subunit I/III interface [polypeptide binding]; other site 399804000490 Subunit III/VIb interface [polypeptide binding]; other site 399804000491 Subunit III/VIa interface; other site 399804000492 Subunit III/Vb interface [polypeptide binding]; other site 399804000493 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 399804000494 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 399804000495 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 399804000496 Subunit I/III interface [polypeptide binding]; other site 399804000497 D-pathway; other site 399804000498 Subunit I/VIIc interface [polypeptide binding]; other site 399804000499 Subunit I/IV interface [polypeptide binding]; other site 399804000500 Subunit I/II interface [polypeptide binding]; other site 399804000501 Low-spin heme (heme a) binding site [chemical binding]; other site 399804000502 Subunit I/VIIa interface [polypeptide binding]; other site 399804000503 Subunit I/VIa interface [polypeptide binding]; other site 399804000504 Dimer interface; other site 399804000505 Putative water exit pathway; other site 399804000506 Binuclear center (heme a3/CuB) [ion binding]; other site 399804000507 K-pathway; other site 399804000508 Subunit I/Vb interface [polypeptide binding]; other site 399804000509 Putative proton exit pathway; other site 399804000510 Subunit I/VIb interface; other site 399804000511 Subunit I/VIc interface [polypeptide binding]; other site 399804000512 Electron transfer pathway; other site 399804000513 Subunit I/VIIIb interface [polypeptide binding]; other site 399804000514 Subunit I/VIIb interface [polypeptide binding]; other site 399804000515 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 399804000516 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 399804000517 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 399804000518 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 399804000519 Cytochrome c; Region: Cytochrom_C; pfam00034 399804000520 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 399804000521 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 399804000522 Cell division inhibitor SulA; Region: SulA; cl01880 399804000523 LexA repressor; Validated; Region: PRK00215 399804000524 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 399804000525 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 399804000526 Catalytic site [active] 399804000527 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 399804000528 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 399804000529 putative acyl-acceptor binding pocket; other site 399804000530 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 399804000531 aromatic amino acid transport protein; Region: araaP; TIGR00837 399804000532 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_prok; cd01062 399804000533 B1 nucleotide binding pocket [chemical binding]; other site 399804000534 B2 nucleotide binding pocket [chemical binding]; other site 399804000535 CAS motifs; other site 399804000536 active site 399804000537 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 399804000538 FAD binding domain; Region: FAD_binding_4; pfam01565 399804000539 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 399804000540 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 399804000541 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 399804000542 dimerization interface [polypeptide binding]; other site 399804000543 putative Zn2+ binding site [ion binding]; other site 399804000544 putative DNA binding site [nucleotide binding]; other site 399804000545 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 399804000546 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 399804000547 pantothenate kinase; Provisional; Region: PRK05439 399804000548 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 399804000549 ATP-binding site [chemical binding]; other site 399804000550 CoA-binding site [chemical binding]; other site 399804000551 Mg2+-binding site [ion binding]; other site 399804000552 elongation factor Tu; Reviewed; Region: PRK00049 399804000553 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 399804000554 G1 box; other site 399804000555 GEF interaction site [polypeptide binding]; other site 399804000556 GTP/Mg2+ binding site [chemical binding]; other site 399804000557 Switch I region; other site 399804000558 G2 box; other site 399804000559 G3 box; other site 399804000560 Switch II region; other site 399804000561 G4 box; other site 399804000562 G5 box; other site 399804000563 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 399804000564 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 399804000565 Antibiotic Binding Site [chemical binding]; other site 399804000566 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 399804000567 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 399804000568 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 399804000569 putative homodimer interface [polypeptide binding]; other site 399804000570 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 399804000571 heterodimer interface [polypeptide binding]; other site 399804000572 homodimer interface [polypeptide binding]; other site 399804000573 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 399804000574 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 399804000575 23S rRNA interface [nucleotide binding]; other site 399804000576 L7/L12 interface [polypeptide binding]; other site 399804000577 putative thiostrepton binding site; other site 399804000578 L25 interface [polypeptide binding]; other site 399804000579 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 399804000580 mRNA/rRNA interface [nucleotide binding]; other site 399804000581 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 399804000582 23S rRNA interface [nucleotide binding]; other site 399804000583 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 399804000584 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 399804000585 core dimer interface [polypeptide binding]; other site 399804000586 peripheral dimer interface [polypeptide binding]; other site 399804000587 L10 interface [polypeptide binding]; other site 399804000588 L11 interface [polypeptide binding]; other site 399804000589 putative EF-Tu interaction site [polypeptide binding]; other site 399804000590 putative EF-G interaction site [polypeptide binding]; other site 399804000591 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 399804000592 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 399804000593 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 399804000594 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 399804000595 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 399804000596 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 399804000597 RPB3 interaction site [polypeptide binding]; other site 399804000598 RPB1 interaction site [polypeptide binding]; other site 399804000599 RPB11 interaction site [polypeptide binding]; other site 399804000600 RPB10 interaction site [polypeptide binding]; other site 399804000601 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 399804000602 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 399804000603 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 399804000604 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 399804000605 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 399804000606 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 399804000607 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 399804000608 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 399804000609 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 399804000610 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 399804000611 DNA binding site [nucleotide binding] 399804000612 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 399804000613 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 399804000614 S17 interaction site [polypeptide binding]; other site 399804000615 S8 interaction site; other site 399804000616 16S rRNA interaction site [nucleotide binding]; other site 399804000617 streptomycin interaction site [chemical binding]; other site 399804000618 23S rRNA interaction site [nucleotide binding]; other site 399804000619 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 399804000620 30S ribosomal protein S7; Validated; Region: PRK05302 399804000621 elongation factor G; Reviewed; Region: PRK00007 399804000622 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 399804000623 G1 box; other site 399804000624 putative GEF interaction site [polypeptide binding]; other site 399804000625 GTP/Mg2+ binding site [chemical binding]; other site 399804000626 Switch I region; other site 399804000627 G2 box; other site 399804000628 G3 box; other site 399804000629 Switch II region; other site 399804000630 G4 box; other site 399804000631 G5 box; other site 399804000632 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 399804000633 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 399804000634 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 399804000635 elongation factor Tu; Reviewed; Region: PRK00049 399804000636 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 399804000637 G1 box; other site 399804000638 GEF interaction site [polypeptide binding]; other site 399804000639 GTP/Mg2+ binding site [chemical binding]; other site 399804000640 Switch I region; other site 399804000641 G2 box; other site 399804000642 G3 box; other site 399804000643 Switch II region; other site 399804000644 G4 box; other site 399804000645 G5 box; other site 399804000646 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 399804000647 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 399804000648 Antibiotic Binding Site [chemical binding]; other site 399804000649 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 399804000650 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 399804000651 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 399804000652 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 399804000653 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 399804000654 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 399804000655 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 399804000656 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 399804000657 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 399804000658 putative translocon binding site; other site 399804000659 protein-rRNA interface [nucleotide binding]; other site 399804000660 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 399804000661 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 399804000662 G-X-X-G motif; other site 399804000663 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 399804000664 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 399804000665 23S rRNA interface [nucleotide binding]; other site 399804000666 5S rRNA interface [nucleotide binding]; other site 399804000667 putative antibiotic binding site [chemical binding]; other site 399804000668 L25 interface [polypeptide binding]; other site 399804000669 L27 interface [polypeptide binding]; other site 399804000670 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 399804000671 23S rRNA interface [nucleotide binding]; other site 399804000672 putative translocon interaction site; other site 399804000673 signal recognition particle (SRP54) interaction site; other site 399804000674 L23 interface [polypeptide binding]; other site 399804000675 trigger factor interaction site; other site 399804000676 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 399804000677 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 399804000678 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 399804000679 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 399804000680 RNA binding site [nucleotide binding]; other site 399804000681 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 399804000682 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 399804000683 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 399804000684 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 399804000685 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 399804000686 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 399804000687 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 399804000688 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 399804000689 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 399804000690 5S rRNA interface [nucleotide binding]; other site 399804000691 23S rRNA interface [nucleotide binding]; other site 399804000692 L5 interface [polypeptide binding]; other site 399804000693 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 399804000694 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 399804000695 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 399804000696 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 399804000697 23S rRNA binding site [nucleotide binding]; other site 399804000698 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 399804000699 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 399804000700 SecY translocase; Region: SecY; pfam00344 399804000701 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 399804000702 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 399804000703 30S ribosomal protein S13; Region: bact_S13; TIGR03631 399804000704 30S ribosomal protein S11; Validated; Region: PRK05309 399804000705 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 399804000706 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 399804000707 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 399804000708 RNA binding surface [nucleotide binding]; other site 399804000709 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 399804000710 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 399804000711 alphaNTD homodimer interface [polypeptide binding]; other site 399804000712 alphaNTD - beta interaction site [polypeptide binding]; other site 399804000713 alphaNTD - beta' interaction site [polypeptide binding]; other site 399804000714 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 399804000715 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 399804000716 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13165 399804000717 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 399804000718 heme exporter protein CcmC; Region: ccmC; TIGR01191 399804000719 heme exporter protein CcmB; Region: ccmB; TIGR01190 399804000720 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 399804000721 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804000722 Walker A/P-loop; other site 399804000723 ATP binding site [chemical binding]; other site 399804000724 Q-loop/lid; other site 399804000725 ABC transporter signature motif; other site 399804000726 Walker B; other site 399804000727 D-loop; other site 399804000728 H-loop/switch region; other site 399804000729 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 399804000730 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 399804000731 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 399804000732 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 399804000733 binding surface 399804000734 TPR motif; other site 399804000735 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 399804000736 thiol:disulfide interchange protein DsbE; Provisional; Region: PRK15412 399804000737 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 399804000738 catalytic residues [active] 399804000739 central insert; other site 399804000740 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 399804000741 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 399804000742 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 399804000743 catalytic residues [active] 399804000744 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 399804000745 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 399804000746 Sodium:sulfate symporter transmembrane region; Region: Na_sulph_symp; pfam00939 399804000747 transmembrane helices; other site 399804000748 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 399804000749 Fumarase C-terminus; Region: Fumerase_C; pfam05683 399804000750 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 399804000751 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 399804000752 active site 399804000753 phosphorylation site [posttranslational modification] 399804000754 intermolecular recognition site; other site 399804000755 dimerization interface [polypeptide binding]; other site 399804000756 HTH domain; Region: HTH_11; pfam08279 399804000757 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 399804000758 PAS domain; Region: PAS; smart00091 399804000759 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 399804000760 ATP binding site [chemical binding]; other site 399804000761 Mg2+ binding site [ion binding]; other site 399804000762 G-X-G motif; other site 399804000763 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 399804000764 Iron-sulfur protein interface; other site 399804000765 proximal quinone binding site [chemical binding]; other site 399804000766 C-subunit interface; other site 399804000767 distal quinone binding site; other site 399804000768 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 399804000769 D-subunit interface [polypeptide binding]; other site 399804000770 Iron-sulfur protein interface; other site 399804000771 proximal quinone binding site [chemical binding]; other site 399804000772 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 399804000773 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 399804000774 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 399804000775 L-aspartate oxidase; Provisional; Region: PRK06175 399804000776 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 399804000777 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804000778 Coenzyme A binding pocket [chemical binding]; other site 399804000779 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804000780 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 399804000781 dimer interface [polypeptide binding]; other site 399804000782 phosphorylation site [posttranslational modification] 399804000783 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 399804000784 ATP binding site [chemical binding]; other site 399804000785 Mg2+ binding site [ion binding]; other site 399804000786 G-X-G motif; other site 399804000787 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804000788 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 399804000789 active site 399804000790 phosphorylation site [posttranslational modification] 399804000791 intermolecular recognition site; other site 399804000792 dimerization interface [polypeptide binding]; other site 399804000793 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 399804000794 DNA binding site [nucleotide binding] 399804000795 Predicted membrane protein [Function unknown]; Region: COG3212 399804000796 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 399804000797 Dihaem cytochrome c; Region: DHC; pfam09626 399804000798 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 399804000799 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 399804000800 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 399804000801 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 399804000802 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 399804000803 NAD(P) binding site [chemical binding]; other site 399804000804 catalytic residues [active] 399804000805 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 399804000806 dimerization interface [polypeptide binding]; other site 399804000807 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 399804000808 dimer interface [polypeptide binding]; other site 399804000809 phosphorylation site [posttranslational modification] 399804000810 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 399804000811 ATP binding site [chemical binding]; other site 399804000812 Mg2+ binding site [ion binding]; other site 399804000813 G-X-G motif; other site 399804000814 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 399804000815 active site 399804000816 phosphorylation site [posttranslational modification] 399804000817 intermolecular recognition site; other site 399804000818 dimerization interface [polypeptide binding]; other site 399804000819 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 399804000820 DNA binding site [nucleotide binding] 399804000821 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 399804000822 dimer interface [polypeptide binding]; other site 399804000823 Cation efflux family; Region: Cation_efflux; cl00316 399804000824 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 399804000825 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 399804000826 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 399804000827 active site 399804000828 phosphorylation site [posttranslational modification] 399804000829 intermolecular recognition site; other site 399804000830 dimerization interface [polypeptide binding]; other site 399804000831 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 399804000832 Walker A motif; other site 399804000833 ATP binding site [chemical binding]; other site 399804000834 Walker B motif; other site 399804000835 arginine finger; other site 399804000836 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804000837 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 399804000838 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 399804000839 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 399804000840 dimer interface [polypeptide binding]; other site 399804000841 phosphorylation site [posttranslational modification] 399804000842 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 399804000843 ATP binding site [chemical binding]; other site 399804000844 Mg2+ binding site [ion binding]; other site 399804000845 G-X-G motif; other site 399804000846 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 399804000847 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 399804000848 N-terminal domain interface [polypeptide binding]; other site 399804000849 dimer interface [polypeptide binding]; other site 399804000850 substrate binding pocket (H-site) [chemical binding]; other site 399804000851 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 399804000852 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 399804000853 putative C-terminal domain interface [polypeptide binding]; other site 399804000854 putative GSH binding site (G-site) [chemical binding]; other site 399804000855 putative dimer interface [polypeptide binding]; other site 399804000856 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 399804000857 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 399804000858 potential catalytic triad [active] 399804000859 conserved cys residue [active] 399804000860 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 399804000861 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 399804000862 dimer interface [polypeptide binding]; other site 399804000863 active site 399804000864 metal binding site [ion binding]; metal-binding site 399804000865 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804000866 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804000867 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 399804000868 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804000869 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804000870 dimer interface [polypeptide binding]; other site 399804000871 putative CheW interface [polypeptide binding]; other site 399804000872 5-histidylcysteine sulfoxide synthase; Region: ovoA_Nterm; TIGR04344 399804000873 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 399804000874 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 399804000875 S-adenosylmethionine binding site [chemical binding]; other site 399804000876 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 399804000877 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 399804000878 substrate binding site [chemical binding]; other site 399804000879 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 399804000880 ATP binding site [chemical binding]; other site 399804000881 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804000882 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804000883 metal binding site [ion binding]; metal-binding site 399804000884 active site 399804000885 I-site; other site 399804000886 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 399804000887 MOSC domain; Region: MOSC; pfam03473 399804000888 3-alpha domain; Region: 3-alpha; pfam03475 399804000889 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296 399804000890 Cache domain; Region: Cache_1; pfam02743 399804000891 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 399804000892 dimerization interface [polypeptide binding]; other site 399804000893 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804000894 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804000895 dimer interface [polypeptide binding]; other site 399804000896 putative CheW interface [polypeptide binding]; other site 399804000897 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 399804000898 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 399804000899 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 399804000900 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 399804000901 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 399804000902 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 399804000903 FeS/SAM binding site; other site 399804000904 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 399804000905 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 399804000906 trimer interface [polypeptide binding]; other site 399804000907 dimer interface [polypeptide binding]; other site 399804000908 putative active site [active] 399804000909 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 399804000910 MoaE interaction surface [polypeptide binding]; other site 399804000911 MoeB interaction surface [polypeptide binding]; other site 399804000912 thiocarboxylated glycine; other site 399804000913 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 399804000914 MoaE homodimer interface [polypeptide binding]; other site 399804000915 MoaD interaction [polypeptide binding]; other site 399804000916 active site residues [active] 399804000917 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 399804000918 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 399804000919 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 399804000920 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 399804000921 dimer interface [polypeptide binding]; other site 399804000922 conserved gate region; other site 399804000923 putative PBP binding loops; other site 399804000924 ABC-ATPase subunit interface; other site 399804000925 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 399804000926 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804000927 Walker A/P-loop; other site 399804000928 ATP binding site [chemical binding]; other site 399804000929 Q-loop/lid; other site 399804000930 ABC transporter signature motif; other site 399804000931 Walker B; other site 399804000932 D-loop; other site 399804000933 H-loop/switch region; other site 399804000934 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 399804000935 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804000936 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 399804000937 active site 399804000938 phosphorylation site [posttranslational modification] 399804000939 intermolecular recognition site; other site 399804000940 dimerization interface [polypeptide binding]; other site 399804000941 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 399804000942 DNA binding site [nucleotide binding] 399804000943 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804000944 HAMP domain; Region: HAMP; pfam00672 399804000945 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 399804000946 dimer interface [polypeptide binding]; other site 399804000947 phosphorylation site [posttranslational modification] 399804000948 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 399804000949 ATP binding site [chemical binding]; other site 399804000950 Mg2+ binding site [ion binding]; other site 399804000951 G-X-G motif; other site 399804000952 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 399804000953 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 399804000954 active site 399804000955 Proteolipid membrane potential modulator; Region: Pmp3; pfam01679 399804000956 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804000957 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 399804000958 N-terminal plug; other site 399804000959 ligand-binding site [chemical binding]; other site 399804000960 Protein of unknown function (DUF2986); Region: DUF2986; pfam11661 399804000961 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 399804000962 Peptidase family M23; Region: Peptidase_M23; pfam01551 399804000963 CHAP domain; Region: CHAP; pfam05257 399804000964 Domain of unknown function (DUF1864); Region: DUF1864; pfam08933 399804000965 kynureninase; Region: kynureninase; TIGR01814 399804000966 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 399804000967 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 399804000968 catalytic residue [active] 399804000969 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804000970 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804000971 L-aspartate oxidase; Provisional; Region: PRK06175 399804000972 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 399804000973 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 399804000974 heme-binding residues [chemical binding]; other site 399804000975 Cupin domain; Region: Cupin_2; cl17218 399804000976 glutamine synthetase; Provisional; Region: glnA; PRK09469 399804000977 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 399804000978 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 399804000979 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 399804000980 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 399804000981 G1 box; other site 399804000982 putative GEF interaction site [polypeptide binding]; other site 399804000983 GTP/Mg2+ binding site [chemical binding]; other site 399804000984 Switch I region; other site 399804000985 G2 box; other site 399804000986 G3 box; other site 399804000987 Switch II region; other site 399804000988 G4 box; other site 399804000989 G5 box; other site 399804000990 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 399804000991 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 399804000992 SnoaL-like domain; Region: SnoaL_3; pfam13474 399804000993 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804000994 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804000995 metal binding site [ion binding]; metal-binding site 399804000996 active site 399804000997 I-site; other site 399804000998 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 399804000999 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 399804001000 dimer interface [polypeptide binding]; other site 399804001001 active site 399804001002 heme binding site [chemical binding]; other site 399804001003 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 399804001004 4Fe-4S binding domain; Region: Fer4_5; pfam12801 399804001005 4Fe-4S binding domain; Region: Fer4_5; pfam12801 399804001006 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 399804001007 hypothetical protein; Reviewed; Region: PRK01637 399804001008 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 399804001009 putative active site [active] 399804001010 dimerization interface [polypeptide binding]; other site 399804001011 putative tRNAtyr binding site [nucleotide binding]; other site 399804001012 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 399804001013 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 399804001014 azoreductase; Reviewed; Region: PRK00170 399804001015 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 399804001016 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 399804001017 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 399804001018 non-specific DNA binding site [nucleotide binding]; other site 399804001019 salt bridge; other site 399804001020 sequence-specific DNA binding site [nucleotide binding]; other site 399804001021 Cupin domain; Region: Cupin_2; pfam07883 399804001022 Benzoate membrane transport protein; Region: BenE; pfam03594 399804001023 benzoate transporter; Region: benE; TIGR00843 399804001024 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804001025 Coenzyme A binding pocket [chemical binding]; other site 399804001026 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 399804001027 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 399804001028 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 399804001029 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 399804001030 dimer interface [polypeptide binding]; other site 399804001031 active site 399804001032 3-oxoacyl-(acyl-carrier-protein) reductase, putative; Region: fabG_rel; TIGR01831 399804001033 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 399804001034 NAD(P) binding site [chemical binding]; other site 399804001035 homotetramer interface [polypeptide binding]; other site 399804001036 homodimer interface [polypeptide binding]; other site 399804001037 active site 399804001038 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 399804001039 putative active site 1 [active] 399804001040 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 399804001041 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 399804001042 dimer interface [polypeptide binding]; other site 399804001043 active site 399804001044 Protein of unknown function (DUF3261); Region: DUF3261; pfam11659 399804001045 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 399804001046 Predicted exporter [General function prediction only]; Region: COG4258 399804001047 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 399804001048 active site 399804001049 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 399804001050 active sites [active] 399804001051 tetramer interface [polypeptide binding]; other site 399804001052 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 399804001053 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 399804001054 Ligand binding site; other site 399804001055 Putative Catalytic site; other site 399804001056 DXD motif; other site 399804001057 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 399804001058 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 399804001059 putative acyl-acceptor binding pocket; other site 399804001060 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 399804001061 active site 2 [active] 399804001062 active site 1 [active] 399804001063 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 399804001064 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 399804001065 acyl-activating enzyme (AAE) consensus motif; other site 399804001066 AMP binding site [chemical binding]; other site 399804001067 active site 399804001068 CoA binding site [chemical binding]; other site 399804001069 Predicted membrane protein [Function unknown]; Region: COG4648 399804001070 acyl carrier protein; Provisional; Region: PRK05350 399804001071 Phosphopantetheine attachment site; Region: PP-binding; cl09936 399804001072 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 399804001073 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 399804001074 putative acyl-acceptor binding pocket; other site 399804001075 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 399804001076 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804001077 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 399804001078 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 399804001079 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 399804001080 generic binding surface II; other site 399804001081 ssDNA binding site; other site 399804001082 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 399804001083 ATP binding site [chemical binding]; other site 399804001084 putative Mg++ binding site [ion binding]; other site 399804001085 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 399804001086 nucleotide binding region [chemical binding]; other site 399804001087 ATP-binding site [chemical binding]; other site 399804001088 inner membrane protein; Provisional; Region: PRK10995 399804001089 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804001090 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 399804001091 ligand binding site [chemical binding]; other site 399804001092 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 399804001093 hypothetical protein; Provisional; Region: PRK11820 399804001094 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 399804001095 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 399804001096 ribonuclease PH; Reviewed; Region: rph; PRK00173 399804001097 Ribonuclease PH; Region: RNase_PH_bact; cd11362 399804001098 hexamer interface [polypeptide binding]; other site 399804001099 active site 399804001100 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 399804001101 active site 399804001102 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 399804001103 GTP cyclohydrolase I; Provisional; Region: PLN03044 399804001104 active site 399804001105 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 399804001106 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804001107 division inhibitor protein; Provisional; Region: slmA; PRK09480 399804001108 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804001109 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 399804001110 trimer interface [polypeptide binding]; other site 399804001111 active site 399804001112 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 399804001113 Flavoprotein; Region: Flavoprotein; pfam02441 399804001114 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 399804001115 hypothetical protein; Reviewed; Region: PRK00024 399804001116 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 399804001117 MPN+ (JAMM) motif; other site 399804001118 Zinc-binding site [ion binding]; other site 399804001119 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 399804001120 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 399804001121 N-acetylglutamate synthase; Validated; Region: PRK05279 399804001122 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 399804001123 putative feedback inhibition sensing region; other site 399804001124 putative nucleotide binding site [chemical binding]; other site 399804001125 putative substrate binding site [chemical binding]; other site 399804001126 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804001127 Coenzyme A binding pocket [chemical binding]; other site 399804001128 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 399804001129 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 399804001130 CoenzymeA binding site [chemical binding]; other site 399804001131 subunit interaction site [polypeptide binding]; other site 399804001132 PHB binding site; other site 399804001133 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 399804001134 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 399804001135 ATP binding site [chemical binding]; other site 399804001136 putative Mg++ binding site [ion binding]; other site 399804001137 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 399804001138 nucleotide binding region [chemical binding]; other site 399804001139 ATP-binding site [chemical binding]; other site 399804001140 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 399804001141 HRDC domain; Region: HRDC; pfam00570 399804001142 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804001143 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804001144 active site 399804001145 I-site; other site 399804001146 metal binding site [ion binding]; metal-binding site 399804001147 2-isopropylmalate synthase; Validated; Region: PRK00915 399804001148 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 399804001149 active site 399804001150 catalytic residues [active] 399804001151 metal binding site [ion binding]; metal-binding site 399804001152 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 399804001153 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 399804001154 tartrate dehydrogenase; Region: TTC; TIGR02089 399804001155 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 399804001156 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 399804001157 substrate binding site [chemical binding]; other site 399804001158 ligand binding site [chemical binding]; other site 399804001159 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 399804001160 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 399804001161 substrate binding site [chemical binding]; other site 399804001162 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 399804001163 glycerol kinase; Provisional; Region: glpK; PRK00047 399804001164 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 399804001165 N- and C-terminal domain interface [polypeptide binding]; other site 399804001166 active site 399804001167 MgATP binding site [chemical binding]; other site 399804001168 catalytic site [active] 399804001169 metal binding site [ion binding]; metal-binding site 399804001170 glycerol binding site [chemical binding]; other site 399804001171 homotetramer interface [polypeptide binding]; other site 399804001172 homodimer interface [polypeptide binding]; other site 399804001173 FBP binding site [chemical binding]; other site 399804001174 protein IIAGlc interface [polypeptide binding]; other site 399804001175 cell division protein MraZ; Reviewed; Region: PRK00326 399804001176 MraZ protein; Region: MraZ; pfam02381 399804001177 MraZ protein; Region: MraZ; pfam02381 399804001178 MraW methylase family; Region: Methyltransf_5; pfam01795 399804001179 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 399804001180 Cell division protein FtsL; Region: FtsL; pfam04999 399804001181 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 399804001182 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 399804001183 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 399804001184 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 399804001185 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 399804001186 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 399804001187 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 399804001188 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 399804001189 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 399804001190 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 399804001191 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 399804001192 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 399804001193 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 399804001194 Mg++ binding site [ion binding]; other site 399804001195 putative catalytic motif [active] 399804001196 putative substrate binding site [chemical binding]; other site 399804001197 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 399804001198 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 399804001199 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 399804001200 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 399804001201 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 399804001202 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 399804001203 active site 399804001204 homodimer interface [polypeptide binding]; other site 399804001205 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 399804001206 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 399804001207 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 399804001208 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 399804001209 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 399804001210 Cell division protein FtsQ; Region: FtsQ; pfam03799 399804001211 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 399804001212 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 399804001213 nucleotide binding site [chemical binding]; other site 399804001214 Cell division protein FtsA; Region: FtsA; pfam14450 399804001215 cell division protein FtsZ; Validated; Region: PRK09330 399804001216 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 399804001217 nucleotide binding site [chemical binding]; other site 399804001218 SulA interaction site; other site 399804001219 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 399804001220 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 399804001221 Protein of unknown function (DUF721); Region: DUF721; cl02324 399804001222 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 399804001223 Peptidase family M23; Region: Peptidase_M23; pfam01551 399804001224 preprotein translocase subunit SecA; Reviewed; Region: PRK13107 399804001225 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 399804001226 ATP binding site [chemical binding]; other site 399804001227 putative Mg++ binding site [ion binding]; other site 399804001228 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 399804001229 SEC-C motif; Region: SEC-C; pfam02810 399804001230 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 399804001231 Sodium Bile acid symporter family; Region: SBF; pfam01758 399804001232 coproporphyrinogen III oxidase; Provisional; Region: PRK08629 399804001233 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 399804001234 FeS/SAM binding site; other site 399804001235 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804001236 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804001237 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804001238 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804001239 Predicted nuclease (RecB family) [General function prediction only]; Region: COG2251 399804001240 Domain of unknown function (DUF4424); Region: DUF4424; pfam14415 399804001241 enterobactin receptor protein; Provisional; Region: PRK13483 399804001242 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 399804001243 N-terminal plug; other site 399804001244 ligand-binding site [chemical binding]; other site 399804001245 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804001246 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804001247 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 399804001248 putative effector binding pocket; other site 399804001249 dimerization interface [polypeptide binding]; other site 399804001250 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 399804001251 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 399804001252 active site 399804001253 nucleophile elbow; other site 399804001254 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 399804001255 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804001256 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 399804001257 substrate binding pocket [chemical binding]; other site 399804001258 dimerization interface [polypeptide binding]; other site 399804001259 EamA-like transporter family; Region: EamA; cl17759 399804001260 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 399804001261 EamA-like transporter family; Region: EamA; pfam00892 399804001262 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 399804001263 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 399804001264 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 399804001265 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804001266 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804001267 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 399804001268 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 399804001269 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 399804001270 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 399804001271 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 399804001272 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 399804001273 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 399804001274 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like2; cd05667 399804001275 metal binding site [ion binding]; metal-binding site 399804001276 putative dimer interface [polypeptide binding]; other site 399804001277 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 399804001278 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 399804001279 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 399804001280 active site 399804001281 substrate-binding site [chemical binding]; other site 399804001282 metal-binding site [ion binding] 399804001283 ATP binding site [chemical binding]; other site 399804001284 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 399804001285 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 399804001286 dimerization interface [polypeptide binding]; other site 399804001287 domain crossover interface; other site 399804001288 redox-dependent activation switch; other site 399804001289 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 399804001290 RNA binding surface [nucleotide binding]; other site 399804001291 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 399804001292 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 399804001293 type II secretion system protein D; Region: type_II_gspD; TIGR02517 399804001294 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 399804001295 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 399804001296 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 399804001297 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 399804001298 type II secretion system protein E; Region: type_II_gspE; TIGR02533 399804001299 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 399804001300 Walker A motif; other site 399804001301 ATP binding site [chemical binding]; other site 399804001302 Walker B motif; other site 399804001303 type II secretion system protein F; Region: GspF; TIGR02120 399804001304 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 399804001305 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 399804001306 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 399804001307 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 399804001308 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 399804001309 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 399804001310 Type II transport protein GspH; Region: GspH; pfam12019 399804001311 type II secretion system protein I; Region: gspI; TIGR01707 399804001312 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 399804001313 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 399804001314 type II secretion system protein J; Region: gspJ; TIGR01711 399804001315 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 399804001316 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 399804001317 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 399804001318 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 399804001319 GspL periplasmic domain; Region: GspL_C; pfam12693 399804001320 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 399804001321 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 399804001322 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 399804001323 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 399804001324 motif II; other site 399804001325 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl17820 399804001326 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 399804001327 Interdomain contacts; other site 399804001328 Cytokine receptor motif; other site 399804001329 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001330 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001331 Ca2+ binding site [ion binding]; other site 399804001332 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001333 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001334 Ca2+ binding site [ion binding]; other site 399804001335 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001336 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001337 Ca2+ binding site [ion binding]; other site 399804001338 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001339 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001340 Ca2+ binding site [ion binding]; other site 399804001341 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001342 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001343 Ca2+ binding site [ion binding]; other site 399804001344 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001345 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001346 Ca2+ binding site [ion binding]; other site 399804001347 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001348 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001349 Ca2+ binding site [ion binding]; other site 399804001350 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001351 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001352 Ca2+ binding site [ion binding]; other site 399804001353 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001354 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001355 Ca2+ binding site [ion binding]; other site 399804001356 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001357 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001358 Ca2+ binding site [ion binding]; other site 399804001359 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001360 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001361 Ca2+ binding site [ion binding]; other site 399804001362 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 399804001363 Cadherin repeat-like domain; Region: CA_like; cl15786 399804001364 Ca2+ binding site [ion binding]; other site 399804001365 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 399804001366 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804001367 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 399804001368 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 399804001369 dimer interface [polypeptide binding]; other site 399804001370 ADP-ribose binding site [chemical binding]; other site 399804001371 active site 399804001372 nudix motif; other site 399804001373 metal binding site [ion binding]; metal-binding site 399804001374 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 399804001375 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 399804001376 active site 399804001377 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 399804001378 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804001379 Coenzyme A binding pocket [chemical binding]; other site 399804001380 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804001381 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804001382 WHG domain; Region: WHG; pfam13305 399804001383 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 399804001384 putative substrate translocation pore; other site 399804001385 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 399804001386 putative acyl-acceptor binding pocket; other site 399804001387 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 399804001388 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 399804001389 active site residue [active] 399804001390 selenophosphate synthetase; Provisional; Region: PRK00943 399804001391 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 399804001392 dimerization interface [polypeptide binding]; other site 399804001393 putative ATP binding site [chemical binding]; other site 399804001394 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 399804001395 Fatty acid desaturase; Region: FA_desaturase; pfam00487 399804001396 Di-iron ligands [ion binding]; other site 399804001397 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 399804001398 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804001399 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 399804001400 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 399804001401 S-adenosylmethionine binding site [chemical binding]; other site 399804001402 glutamate racemase; Provisional; Region: PRK00865 399804001403 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 399804001404 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 399804001405 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 399804001406 dimer interface [polypeptide binding]; other site 399804001407 allosteric magnesium binding site [ion binding]; other site 399804001408 active site 399804001409 aspartate-rich active site metal binding site; other site 399804001410 Schiff base residues; other site 399804001411 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 399804001412 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 399804001413 hypothetical protein; Region: PHA02277 399804001414 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804001415 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804001416 metal binding site [ion binding]; metal-binding site 399804001417 active site 399804001418 I-site; other site 399804001419 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 399804001420 active site 399804001421 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 399804001422 sec-independent translocase; Provisional; Region: PRK01770 399804001423 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 399804001424 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 399804001425 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 399804001426 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 399804001427 SCP-2 sterol transfer family; Region: SCP2; pfam02036 399804001428 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 399804001429 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 399804001430 S-adenosylmethionine binding site [chemical binding]; other site 399804001431 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 399804001432 putative active site [active] 399804001433 putative metal binding site [ion binding]; other site 399804001434 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 399804001435 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 399804001436 PAP2 superfamily; Region: PAP2; pfam01569 399804001437 active site 399804001438 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 399804001439 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 399804001440 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804001441 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804001442 dimer interface [polypeptide binding]; other site 399804001443 putative CheW interface [polypeptide binding]; other site 399804001444 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804001445 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 399804001446 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 399804001447 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 399804001448 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 399804001449 DHHA2 domain; Region: DHHA2; pfam02833 399804001450 Domain of unknown function (DUF386); Region: DUF386; cl01047 399804001451 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804001452 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 399804001453 N-terminal plug; other site 399804001454 ligand-binding site [chemical binding]; other site 399804001455 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 399804001456 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 399804001457 Pseudouridine synthase, a subgroup of the RluA family; Region: PSRA_1; cd02558 399804001458 probable active site [active] 399804001459 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 399804001460 ATP binding site [chemical binding]; other site 399804001461 Mg2+ binding site [ion binding]; other site 399804001462 G-X-G motif; other site 399804001463 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 399804001464 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 399804001465 active site 399804001466 phosphorylation site [posttranslational modification] 399804001467 intermolecular recognition site; other site 399804001468 dimerization interface [polypeptide binding]; other site 399804001469 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804001470 C factor cell-cell signaling protein; Provisional; Region: PRK09009 399804001471 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 399804001472 NADP binding site [chemical binding]; other site 399804001473 homodimer interface [polypeptide binding]; other site 399804001474 active site 399804001475 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 399804001476 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 399804001477 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 399804001478 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 399804001479 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 399804001480 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 399804001481 Walker A motif; other site 399804001482 ATP binding site [chemical binding]; other site 399804001483 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 399804001484 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 399804001485 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 399804001486 active site 399804001487 HslU subunit interaction site [polypeptide binding]; other site 399804001488 RibD C-terminal domain; Region: RibD_C; cl17279 399804001489 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 399804001490 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 399804001491 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 399804001492 active site 399804001493 phosphorylation site [posttranslational modification] 399804001494 intermolecular recognition site; other site 399804001495 dimerization interface [polypeptide binding]; other site 399804001496 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 399804001497 DNA binding residues [nucleotide binding] 399804001498 dimerization interface [polypeptide binding]; other site 399804001499 Homeodomain-like domain; Region: HTH_23; pfam13384 399804001500 Winged helix-turn helix; Region: HTH_29; pfam13551 399804001501 Winged helix-turn helix; Region: HTH_33; pfam13592 399804001502 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804001503 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804001504 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 399804001505 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 399804001506 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 399804001507 ATP binding site [chemical binding]; other site 399804001508 Mg2+ binding site [ion binding]; other site 399804001509 G-X-G motif; other site 399804001510 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 399804001511 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 399804001512 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 399804001513 substrate binding pocket [chemical binding]; other site 399804001514 membrane-bound complex binding site; other site 399804001515 hinge residues; other site 399804001516 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 399804001517 Sel1-like repeats; Region: SEL1; smart00671 399804001518 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 399804001519 Mechanosensitive ion channel; Region: MS_channel; pfam00924 399804001520 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 399804001521 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 399804001522 dimer interface [polypeptide binding]; other site 399804001523 active site 399804001524 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 399804001525 catalytic residues [active] 399804001526 substrate binding site [chemical binding]; other site 399804001527 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 399804001528 uridine phosphorylase; Provisional; Region: PRK11178 399804001529 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 399804001530 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804001531 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 399804001532 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 399804001533 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 399804001534 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 399804001535 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 399804001536 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 399804001537 Sporulation related domain; Region: SPOR; pfam05036 399804001538 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 399804001539 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 399804001540 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 399804001541 active site 399804001542 HIGH motif; other site 399804001543 KMSK motif region; other site 399804001544 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 399804001545 tRNA binding surface [nucleotide binding]; other site 399804001546 anticodon binding site; other site 399804001547 primosome assembly protein PriA; Validated; Region: PRK05580 399804001548 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 399804001549 ATP binding site [chemical binding]; other site 399804001550 putative Mg++ binding site [ion binding]; other site 399804001551 helicase superfamily c-terminal domain; Region: HELICc; smart00490 399804001552 FimV N-terminal domain; Region: FimV_core; TIGR03505 399804001553 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 399804001554 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 399804001555 Malic enzyme, N-terminal domain; Region: malic; pfam00390 399804001556 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 399804001557 putative NAD(P) binding site [chemical binding]; other site 399804001558 regulatory protein CsrD; Provisional; Region: PRK11059 399804001559 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804001560 metal binding site [ion binding]; metal-binding site 399804001561 active site 399804001562 I-site; other site 399804001563 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 399804001564 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 399804001565 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 399804001566 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 399804001567 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 399804001568 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 399804001569 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 399804001570 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 399804001571 Walker A motif; other site 399804001572 ATP binding site [chemical binding]; other site 399804001573 Walker B motif; other site 399804001574 arginine finger; other site 399804001575 TPR repeat; Region: TPR_11; pfam13414 399804001576 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 399804001577 TPR motif; other site 399804001578 binding surface 399804001579 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 399804001580 binding surface 399804001581 TPR motif; other site 399804001582 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 399804001583 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 399804001584 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 399804001585 Walker A motif; other site 399804001586 ATP binding site [chemical binding]; other site 399804001587 Walker B motif; other site 399804001588 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 399804001589 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 399804001590 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 399804001591 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 399804001592 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 399804001593 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 399804001594 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 399804001595 VcfQ bacterial pilus biogenesis protein, lectin domain; Region: lectin_VcfQ; cd06900 399804001596 putative metal binding site [ion binding]; other site 399804001597 rod shape-determining protein MreB; Provisional; Region: PRK13927 399804001598 MreB and similar proteins; Region: MreB_like; cd10225 399804001599 nucleotide binding site [chemical binding]; other site 399804001600 Mg binding site [ion binding]; other site 399804001601 putative protofilament interaction site [polypeptide binding]; other site 399804001602 RodZ interaction site [polypeptide binding]; other site 399804001603 rod shape-determining protein MreC; Region: mreC; TIGR00219 399804001604 rod shape-determining protein MreC; Region: MreC; pfam04085 399804001605 rod shape-determining protein MreD; Region: MreD; cl01087 399804001606 Maf-like protein; Region: Maf; pfam02545 399804001607 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 399804001608 active site 399804001609 dimer interface [polypeptide binding]; other site 399804001610 ribonuclease G; Provisional; Region: PRK11712 399804001611 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 399804001612 homodimer interface [polypeptide binding]; other site 399804001613 oligonucleotide binding site [chemical binding]; other site 399804001614 TIGR02099 family protein; Region: TIGR02099 399804001615 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 399804001616 nitrilase; Region: PLN02798 399804001617 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 399804001618 putative active site [active] 399804001619 catalytic triad [active] 399804001620 dimer interface [polypeptide binding]; other site 399804001621 protease TldD; Provisional; Region: tldD; PRK10735 399804001622 Outer membrane efflux protein; Region: OEP; pfam02321 399804001623 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 399804001624 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804001625 ABC exporter membrane fusion protein, DevB family; Region: heterocyst_DevB; TIGR02971 399804001626 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804001627 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 399804001628 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 399804001629 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 399804001630 ABC-2 type transporter; Region: ABC2_membrane; cl17235 399804001631 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 399804001632 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 399804001633 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804001634 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804001635 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 399804001636 ApbE family; Region: ApbE; pfam02424 399804001637 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 399804001638 hydroperoxidase II; Provisional; Region: katE; PRK11249 399804001639 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 399804001640 tetramer interface [polypeptide binding]; other site 399804001641 heme binding pocket [chemical binding]; other site 399804001642 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 399804001643 domain interactions; other site 399804001644 MgtC family; Region: MgtC; pfam02308 399804001645 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 399804001646 hypothetical protein; Provisional; Region: PRK05255 399804001647 peptidase PmbA; Provisional; Region: PRK11040 399804001648 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 399804001649 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 399804001650 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 399804001651 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 399804001652 substrate binding pocket [chemical binding]; other site 399804001653 membrane-bound complex binding site; other site 399804001654 Domain of unknown function; Region: DUF331; pfam03889 399804001655 fumarate hydratase; Reviewed; Region: fumC; PRK00485 399804001656 Class II fumarases; Region: Fumarase_classII; cd01362 399804001657 active site 399804001658 tetramer interface [polypeptide binding]; other site 399804001659 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 399804001660 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 399804001661 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 399804001662 FeS/SAM binding site; other site 399804001663 Uncharacterized conserved protein [Function unknown]; Region: COG2968 399804001664 oxidative stress defense protein; Provisional; Region: PRK11087 399804001665 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 399804001666 Methyltransferase domain; Region: Methyltransf_23; pfam13489 399804001667 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 399804001668 S-adenosylmethionine binding site [chemical binding]; other site 399804001669 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 399804001670 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 399804001671 N-terminal plug; other site 399804001672 ligand-binding site [chemical binding]; other site 399804001673 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 399804001674 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804001675 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804001676 EAL domain; Region: EAL; pfam00563 399804001677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804001678 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804001679 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804001680 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804001681 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 399804001682 ATP binding site [chemical binding]; other site 399804001683 active site 399804001684 substrate binding site [chemical binding]; other site 399804001685 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 399804001686 thiosulfate reductase PhsA; Provisional; Region: PRK15488 399804001687 The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_Thiosulfate-R-like; cd02755 399804001688 putative [Fe4-S4] binding site [ion binding]; other site 399804001689 putative molybdopterin cofactor binding site [chemical binding]; other site 399804001690 The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_CT_Thiosulfate-R-like; cd02778 399804001691 putative molybdopterin cofactor binding site; other site 399804001692 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 399804001693 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 399804001694 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 399804001695 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 399804001696 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 399804001697 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 399804001698 dimerization interface [polypeptide binding]; other site 399804001699 DNA binding site [nucleotide binding] 399804001700 corepressor binding sites; other site 399804001701 O-succinylhomoserine (thiol)-lyase; Region: O_succ_thio_ly; TIGR02080 399804001702 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 399804001703 homodimer interface [polypeptide binding]; other site 399804001704 substrate-cofactor binding pocket; other site 399804001705 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804001706 catalytic residue [active] 399804001707 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 399804001708 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 399804001709 nucleotide binding site [chemical binding]; other site 399804001710 substrate binding site [chemical binding]; other site 399804001711 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 399804001712 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 399804001713 FAD binding site [chemical binding]; other site 399804001714 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 399804001715 dimerization interface [polypeptide binding]; other site 399804001716 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804001717 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804001718 dimer interface [polypeptide binding]; other site 399804001719 putative CheW interface [polypeptide binding]; other site 399804001720 transcriptional regulator SlyA; Provisional; Region: PRK03573 399804001721 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 399804001722 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 399804001723 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804001724 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804001725 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 399804001726 Ethanolamine utilisation protein, EutH; Region: EutH; cl01248 399804001727 Cytochrome c; Region: Cytochrom_C; cl11414 399804001728 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 399804001729 Cytochrome c; Region: Cytochrom_C; cl11414 399804001730 Cytochrome c [Energy production and conversion]; Region: COG3258 399804001731 Cytochrome c; Region: Cytochrom_C; pfam00034 399804001732 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 399804001733 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 399804001734 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 399804001735 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 399804001736 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 399804001737 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 399804001738 This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted...; Region: MopB_DmsA-EC; cd02770 399804001739 putative [Fe4-S4] binding site [ion binding]; other site 399804001740 putative molybdopterin cofactor binding site [chemical binding]; other site 399804001741 The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted...; Region: MopB_CT_DmsA-EC; cd02794 399804001742 putative molybdopterin cofactor binding site; other site 399804001743 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 399804001744 4Fe-4S binding domain; Region: Fer4; cl02805 399804001745 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 399804001746 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 399804001747 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 399804001748 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 399804001749 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 399804001750 EamA-like transporter family; Region: EamA; pfam00892 399804001751 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 399804001752 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 399804001753 active site 399804001754 motif I; other site 399804001755 motif II; other site 399804001756 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 399804001757 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 399804001758 ATP binding site [chemical binding]; other site 399804001759 Mg++ binding site [ion binding]; other site 399804001760 motif III; other site 399804001761 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 399804001762 nucleotide binding region [chemical binding]; other site 399804001763 ATP-binding site [chemical binding]; other site 399804001764 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 399804001765 putative RNA binding site [nucleotide binding]; other site 399804001766 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 399804001767 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 399804001768 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 399804001769 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 399804001770 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 399804001771 Major Facilitator Superfamily; Region: MFS_1; pfam07690 399804001772 putative substrate translocation pore; other site 399804001773 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 399804001774 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 399804001775 dimer interface [polypeptide binding]; other site 399804001776 ssDNA binding site [nucleotide binding]; other site 399804001777 tetramer (dimer of dimers) interface [polypeptide binding]; other site 399804001778 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 399804001779 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 399804001780 glutamine binding [chemical binding]; other site 399804001781 catalytic triad [active] 399804001782 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 399804001783 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804001784 HDOD domain; Region: HDOD; pfam08668 399804001785 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 399804001786 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 399804001787 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 399804001788 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 399804001789 inhibitor-cofactor binding pocket; inhibition site 399804001790 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804001791 catalytic residue [active] 399804001792 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 399804001793 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 399804001794 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 399804001795 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 399804001796 NAD(P) binding site [chemical binding]; other site 399804001797 catalytic residues [active] 399804001798 Domain of unknown function (DUF1338); Region: DUF1338; pfam07063 399804001799 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804001800 HAMP domain; Region: HAMP; pfam00672 399804001801 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 399804001802 dimer interface [polypeptide binding]; other site 399804001803 phosphorylation site [posttranslational modification] 399804001804 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 399804001805 ATP binding site [chemical binding]; other site 399804001806 Mg2+ binding site [ion binding]; other site 399804001807 G-X-G motif; other site 399804001808 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804001809 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 399804001810 active site 399804001811 phosphorylation site [posttranslational modification] 399804001812 intermolecular recognition site; other site 399804001813 dimerization interface [polypeptide binding]; other site 399804001814 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 399804001815 DNA binding site [nucleotide binding] 399804001816 Predicted membrane protein [Function unknown]; Region: COG3212 399804001817 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 399804001818 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 399804001819 ligand binding site [chemical binding]; other site 399804001820 flexible hinge region; other site 399804001821 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 399804001822 putative switch regulator; other site 399804001823 non-specific DNA interactions [nucleotide binding]; other site 399804001824 DNA binding site [nucleotide binding] 399804001825 sequence specific DNA binding site [nucleotide binding]; other site 399804001826 putative cAMP binding site [chemical binding]; other site 399804001827 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 399804001828 Sel1-like repeats; Region: SEL1; smart00671 399804001829 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 399804001830 binding surface 399804001831 TPR motif; other site 399804001832 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804001833 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804001834 metal binding site [ion binding]; metal-binding site 399804001835 active site 399804001836 I-site; other site 399804001837 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 399804001838 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 399804001839 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 399804001840 ATP binding site [chemical binding]; other site 399804001841 putative Mg++ binding site [ion binding]; other site 399804001842 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 399804001843 nucleotide binding region [chemical binding]; other site 399804001844 Helicase associated domain (HA2) Add an annotation; Region: HA2; smart00847 399804001845 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 399804001846 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 399804001847 Transglycosylase; Region: Transgly; pfam00912 399804001848 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 399804001849 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 399804001850 Putative integral membrane protein (DUF2391); Region: DUF2391; cl01935 399804001851 Protein of unknown function (DUF3581); Region: DUF3581; pfam12119 399804001852 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 399804001853 PAS domain; Region: PAS_9; pfam13426 399804001854 putative active site [active] 399804001855 heme pocket [chemical binding]; other site 399804001856 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 399804001857 PAS domain; Region: PAS_9; pfam13426 399804001858 putative active site [active] 399804001859 heme pocket [chemical binding]; other site 399804001860 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804001861 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804001862 dimer interface [polypeptide binding]; other site 399804001863 putative CheW interface [polypeptide binding]; other site 399804001864 tetrathionate reductase subunit A; Provisional; Region: PRK14991 399804001865 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 399804001866 molybdopterin cofactor binding site; other site 399804001867 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 399804001868 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 399804001869 putative molybdopterin cofactor binding site; other site 399804001870 tetrathionate reductase subunit C; Provisional; Region: PRK14992 399804001871 tetrathionate reductase subunit B; Provisional; Region: PRK14993 399804001872 4Fe-4S binding domain; Region: Fer4; pfam00037 399804001873 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 399804001874 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 399804001875 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804001876 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 399804001877 dimer interface [polypeptide binding]; other site 399804001878 phosphorylation site [posttranslational modification] 399804001879 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 399804001880 ATP binding site [chemical binding]; other site 399804001881 Mg2+ binding site [ion binding]; other site 399804001882 G-X-G motif; other site 399804001883 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 399804001884 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 399804001885 active site 399804001886 phosphorylation site [posttranslational modification] 399804001887 intermolecular recognition site; other site 399804001888 dimerization interface [polypeptide binding]; other site 399804001889 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 399804001890 DNA binding residues [nucleotide binding] 399804001891 dimerization interface [polypeptide binding]; other site 399804001892 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 399804001893 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 399804001894 active site 399804001895 metal binding site [ion binding]; metal-binding site 399804001896 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 399804001897 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 399804001898 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 399804001899 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804001900 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804001901 dimer interface [polypeptide binding]; other site 399804001902 putative CheW interface [polypeptide binding]; other site 399804001903 hypothetical protein; Provisional; Region: PRK05208 399804001904 BON domain; Region: BON; pfam04972 399804001905 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 399804001906 Nuclease-related domain; Region: NERD; pfam08378 399804001907 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 399804001908 AMP binding site [chemical binding]; other site 399804001909 metal binding site [ion binding]; metal-binding site 399804001910 active site 399804001911 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 399804001912 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 399804001913 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804001914 two-component response regulator; Provisional; Region: PRK11173 399804001915 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 399804001916 active site 399804001917 phosphorylation site [posttranslational modification] 399804001918 intermolecular recognition site; other site 399804001919 dimerization interface [polypeptide binding]; other site 399804001920 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 399804001921 DNA binding site [nucleotide binding] 399804001922 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 399804001923 aspartate kinase III; Validated; Region: PRK09084 399804001924 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 399804001925 nucleotide binding site [chemical binding]; other site 399804001926 substrate binding site [chemical binding]; other site 399804001927 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC-like_1; cd04912 399804001928 dimer interface [polypeptide binding]; other site 399804001929 allosteric regulatory binding pocket; other site 399804001930 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 399804001931 dimer interface [polypeptide binding]; other site 399804001932 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 399804001933 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 399804001934 Cl binding site [ion binding]; other site 399804001935 oligomer interface [polypeptide binding]; other site 399804001936 Uncharacterized protein family (UPF0231); Region: UPF0231; pfam06062 399804001937 transcriptional regulator NarL; Provisional; Region: PRK10651 399804001938 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 399804001939 active site 399804001940 phosphorylation site [posttranslational modification] 399804001941 intermolecular recognition site; other site 399804001942 dimerization interface [polypeptide binding]; other site 399804001943 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 399804001944 DNA binding residues [nucleotide binding] 399804001945 dimerization interface [polypeptide binding]; other site 399804001946 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 399804001947 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 399804001948 HAMP domain; Region: HAMP; pfam00672 399804001949 Histidine kinase; Region: HisKA_3; pfam07730 399804001950 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 399804001951 ATP binding site [chemical binding]; other site 399804001952 Mg2+ binding site [ion binding]; other site 399804001953 G-X-G motif; other site 399804001954 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 399804001955 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 399804001956 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804001957 Q-loop/lid; other site 399804001958 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804001959 ABC transporter signature motif; other site 399804001960 ABC transporter signature motif; other site 399804001961 Walker B; other site 399804001962 Walker B; other site 399804001963 D-loop; other site 399804001964 D-loop; other site 399804001965 H-loop/switch region; other site 399804001966 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804001967 Walker A/P-loop; other site 399804001968 ATP binding site [chemical binding]; other site 399804001969 Q-loop/lid; other site 399804001970 ABC transporter signature motif; other site 399804001971 Walker B; other site 399804001972 D-loop; other site 399804001973 H-loop/switch region; other site 399804001974 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl17257 399804001975 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 399804001976 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 399804001977 catalytic residues [active] 399804001978 Predicted transcriptional regulators [Transcription]; Region: COG1695 399804001979 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 399804001980 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804001981 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 399804001982 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 399804001983 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804001984 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 399804001985 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804001986 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 399804001987 SnoaL-like domain; Region: SnoaL_2; pfam12680 399804001988 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804001989 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804001990 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804001991 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804001992 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804001993 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 399804001994 putative effector binding pocket; other site 399804001995 dimerization interface [polypeptide binding]; other site 399804001996 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 399804001997 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 399804001998 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 399804001999 oligomerisation interface [polypeptide binding]; other site 399804002000 mobile loop; other site 399804002001 roof hairpin; other site 399804002002 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 399804002003 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 399804002004 ring oligomerisation interface [polypeptide binding]; other site 399804002005 ATP/Mg binding site [chemical binding]; other site 399804002006 stacking interactions; other site 399804002007 hinge regions; other site 399804002008 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 399804002009 Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning]; Region: RIO1; COG1718 399804002010 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 399804002011 ATP binding site [chemical binding]; other site 399804002012 Transposase; Region: HTH_Tnp_1; cl17663 399804002013 putative outer membrane lipoprotein; Provisional; Region: PRK10510 399804002014 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804002015 ligand binding site [chemical binding]; other site 399804002016 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 399804002017 molybdate ABC transporter periplasmic molybdate-binding protein; Provisional; Region: PRK03537 399804002018 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 399804002019 MgtE intracellular N domain; Region: MgtE_N; smart00924 399804002020 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 399804002021 Divalent cation transporter; Region: MgtE; cl00786 399804002022 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 399804002023 dimerization domain swap beta strand [polypeptide binding]; other site 399804002024 regulatory protein interface [polypeptide binding]; other site 399804002025 active site 399804002026 regulatory phosphorylation site [posttranslational modification]; other site 399804002027 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 399804002028 AAA domain; Region: AAA_18; pfam13238 399804002029 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 399804002030 active site 399804002031 phosphorylation site [posttranslational modification] 399804002032 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 399804002033 30S subunit binding site; other site 399804002034 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 399804002035 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 399804002036 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 399804002037 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 399804002038 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 399804002039 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 399804002040 Walker A/P-loop; other site 399804002041 ATP binding site [chemical binding]; other site 399804002042 Q-loop/lid; other site 399804002043 ABC transporter signature motif; other site 399804002044 Walker B; other site 399804002045 D-loop; other site 399804002046 H-loop/switch region; other site 399804002047 OstA-like protein; Region: OstA; cl00844 399804002048 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 399804002049 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 399804002050 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 399804002051 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 399804002052 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 399804002053 active site 399804002054 motif I; other site 399804002055 motif II; other site 399804002056 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 399804002057 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 399804002058 putative active site [active] 399804002059 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 399804002060 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 399804002061 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 399804002062 Walker A/P-loop; other site 399804002063 ATP binding site [chemical binding]; other site 399804002064 Q-loop/lid; other site 399804002065 ABC transporter signature motif; other site 399804002066 Walker B; other site 399804002067 D-loop; other site 399804002068 H-loop/switch region; other site 399804002069 Permease; Region: Permease; cl00510 399804002070 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 399804002071 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 399804002072 mce related protein; Region: MCE; pfam02470 399804002073 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 399804002074 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 399804002075 anti sigma factor interaction site; other site 399804002076 regulatory phosphorylation site [posttranslational modification]; other site 399804002077 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 399804002078 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 399804002079 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 399804002080 hinge; other site 399804002081 active site 399804002082 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 399804002083 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 399804002084 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 399804002085 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 399804002086 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 399804002087 homodimer interface [polypeptide binding]; other site 399804002088 substrate-cofactor binding pocket; other site 399804002089 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804002090 catalytic residue [active] 399804002091 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 399804002092 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 399804002093 Walker A/P-loop; other site 399804002094 ATP binding site [chemical binding]; other site 399804002095 Q-loop/lid; other site 399804002096 ABC transporter signature motif; other site 399804002097 Walker B; other site 399804002098 D-loop; other site 399804002099 H-loop/switch region; other site 399804002100 TOBE-like domain; Region: TOBE_3; pfam12857 399804002101 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 399804002102 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 399804002103 dimer interface [polypeptide binding]; other site 399804002104 conserved gate region; other site 399804002105 putative PBP binding loops; other site 399804002106 ABC-ATPase subunit interface; other site 399804002107 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 399804002108 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 399804002109 dimer interface [polypeptide binding]; other site 399804002110 conserved gate region; other site 399804002111 putative PBP binding loops; other site 399804002112 ABC-ATPase subunit interface; other site 399804002113 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 399804002114 PBP superfamily domain; Region: PBP_like; cl17867 399804002115 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 399804002116 membrane-bound complex binding site; other site 399804002117 hinge residues; other site 399804002118 Uncharacterized small protein (DUF2292); Region: DUF2292; pfam10055 399804002119 Serine hydrolase; Region: Ser_hydrolase; pfam06821 399804002120 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 399804002121 His-Xaa-Ser system protein HsxD; Region: chp_LLNDYxLRE; TIGR03976 399804002122 His-Xaa-Ser system radical SAM maturase HxsB; Region: rSAM_paired_1; TIGR03978 399804002123 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 399804002124 FeS/SAM binding site; other site 399804002125 HSF-type DNA-binding; Region: HSF_DNA-bind; cl12113 399804002126 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 399804002127 His-Xaa-Ser system radical SAM maturase HxsC; Region: rSAM_pair_HxsC; TIGR03977 399804002128 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 399804002129 FeS/SAM binding site; other site 399804002130 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 399804002131 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 399804002132 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 399804002133 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 399804002134 protein binding site [polypeptide binding]; other site 399804002135 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 399804002136 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 399804002137 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 399804002138 protein binding site [polypeptide binding]; other site 399804002139 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 399804002140 Predicted ATPase [General function prediction only]; Region: COG1485 399804002141 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 399804002142 23S rRNA interface [nucleotide binding]; other site 399804002143 L3 interface [polypeptide binding]; other site 399804002144 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 399804002145 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 399804002146 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 399804002147 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 399804002148 GDP-binding site [chemical binding]; other site 399804002149 ACT binding site; other site 399804002150 IMP binding site; other site 399804002151 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 399804002152 Sel1-like repeats; Region: SEL1; smart00671 399804002153 exoribonuclease R; Provisional; Region: PRK11642 399804002154 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 399804002155 RNB domain; Region: RNB; pfam00773 399804002156 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 399804002157 RNA binding site [nucleotide binding]; other site 399804002158 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 399804002159 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 399804002160 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 399804002161 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 399804002162 Major Facilitator Superfamily; Region: MFS_1; pfam07690 399804002163 putative substrate translocation pore; other site 399804002164 Protein of unknown function, DUF481; Region: DUF481; pfam04338 399804002165 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 399804002166 primosomal replication protein N; Provisional; Region: PRK02801 399804002167 generic binding surface II; other site 399804002168 generic binding surface I; other site 399804002169 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 399804002170 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 399804002171 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 399804002172 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 399804002173 Peptidase S46; Region: Peptidase_S46; pfam10459 399804002174 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 399804002175 replicative DNA helicase; Provisional; Region: PRK08006 399804002176 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 399804002177 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 399804002178 Walker A motif; other site 399804002179 ATP binding site [chemical binding]; other site 399804002180 Walker B motif; other site 399804002181 DNA binding loops [nucleotide binding] 399804002182 alanine racemase; Reviewed; Region: alr; PRK00053 399804002183 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 399804002184 active site 399804002185 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 399804002186 substrate binding site [chemical binding]; other site 399804002187 catalytic residues [active] 399804002188 dimer interface [polypeptide binding]; other site 399804002189 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 399804002190 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 399804002191 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 399804002192 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 399804002193 FMN binding site [chemical binding]; other site 399804002194 active site 399804002195 catalytic residues [active] 399804002196 substrate binding site [chemical binding]; other site 399804002197 PspC domain; Region: PspC; pfam04024 399804002198 enoyl-CoA hydratase; Provisional; Region: PRK06688 399804002199 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 399804002200 substrate binding site [chemical binding]; other site 399804002201 oxyanion hole (OAH) forming residues; other site 399804002202 trimer interface [polypeptide binding]; other site 399804002203 Protein of unknown function (DUF461); Region: DUF461; pfam04314 399804002204 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; pfam10095 399804002205 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 399804002206 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 399804002207 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 399804002208 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 399804002209 dimer interface [polypeptide binding]; other site 399804002210 ADP-ribose binding site [chemical binding]; other site 399804002211 active site 399804002212 nudix motif; other site 399804002213 metal binding site [ion binding]; metal-binding site 399804002214 Protein of unknown function (DUF1249); Region: DUF1249; pfam06853 399804002215 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 399804002216 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 399804002217 active site 399804002218 metal binding site [ion binding]; metal-binding site 399804002219 hexamer interface [polypeptide binding]; other site 399804002220 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 399804002221 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 399804002222 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 399804002223 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 399804002224 ATP binding site [chemical binding]; other site 399804002225 Mg2+ binding site [ion binding]; other site 399804002226 G-X-G motif; other site 399804002227 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 399804002228 anchoring element; other site 399804002229 dimer interface [polypeptide binding]; other site 399804002230 ATP binding site [chemical binding]; other site 399804002231 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 399804002232 active site 399804002233 metal binding site [ion binding]; metal-binding site 399804002234 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 399804002235 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 399804002236 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 399804002237 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 399804002238 CAP-like domain; other site 399804002239 active site 399804002240 primary dimer interface [polypeptide binding]; other site 399804002241 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 399804002242 active site 399804002243 catalytic residues [active] 399804002244 DNA binding site [nucleotide binding] 399804002245 Int/Topo IB signature motif; other site 399804002246 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 399804002247 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804002248 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 399804002249 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804002250 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804002251 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804002252 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804002253 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 399804002254 Predicted transcriptional regulators [Transcription]; Region: COG1733 399804002255 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 399804002256 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 399804002257 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 399804002258 putative C-terminal domain interface [polypeptide binding]; other site 399804002259 putative GSH binding site (G-site) [chemical binding]; other site 399804002260 putative dimer interface [polypeptide binding]; other site 399804002261 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 399804002262 N-terminal domain interface [polypeptide binding]; other site 399804002263 dimer interface [polypeptide binding]; other site 399804002264 substrate binding pocket (H-site) [chemical binding]; other site 399804002265 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 399804002266 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl17257 399804002267 DNA binding residues [nucleotide binding] 399804002268 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 399804002269 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 399804002270 heme exporter protein CcmC; Region: ccmC; TIGR01191 399804002271 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 399804002272 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 399804002273 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 399804002274 non-specific DNA binding site [nucleotide binding]; other site 399804002275 salt bridge; other site 399804002276 sequence-specific DNA binding site [nucleotide binding]; other site 399804002277 Family description; Region: UvrD_C_2; pfam13538 399804002278 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 399804002279 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 399804002280 non-specific DNA binding site [nucleotide binding]; other site 399804002281 salt bridge; other site 399804002282 sequence-specific DNA binding site [nucleotide binding]; other site 399804002283 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 399804002284 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 399804002285 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 399804002286 E3 interaction surface; other site 399804002287 lipoyl attachment site [posttranslational modification]; other site 399804002288 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804002289 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 399804002290 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]; Region: MecR1; COG4219 399804002291 Penicillinase repressor; Region: Pencillinase_R; cl17580 399804002292 hypothetical protein; Provisional; Region: PRK09272 399804002293 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 399804002294 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 399804002295 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 399804002296 putative active site [active] 399804002297 putative NTP binding site [chemical binding]; other site 399804002298 putative nucleic acid binding site [nucleotide binding]; other site 399804002299 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 399804002300 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 399804002301 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 399804002302 putative active site [active] 399804002303 putative NTP binding site [chemical binding]; other site 399804002304 putative nucleic acid binding site [nucleotide binding]; other site 399804002305 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 399804002306 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 399804002307 integron integrase; Region: integrase_gron; TIGR02249 399804002308 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 399804002309 Int/Topo IB signature motif; other site 399804002310 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 399804002311 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 399804002312 active site 399804002313 DNA binding site [nucleotide binding] 399804002314 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 399804002315 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 399804002316 Catalytic site [active] 399804002317 YecR-like lipoprotein; Region: YecR; cl10256 399804002318 Transposase; Region: HTH_Tnp_1; pfam01527 399804002319 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 399804002320 putative transposase OrfB; Reviewed; Region: PHA02517 399804002321 HTH-like domain; Region: HTH_21; pfam13276 399804002322 Integrase core domain; Region: rve; pfam00665 399804002323 Integrase core domain; Region: rve_2; pfam13333 399804002324 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 399804002325 Part of AAA domain; Region: AAA_19; pfam13245 399804002326 Family description; Region: UvrD_C_2; pfam13538 399804002327 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 399804002328 active site 399804002329 catalytic residues [active] 399804002330 DNA binding site [nucleotide binding] 399804002331 Int/Topo IB signature motif; other site 399804002332 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 399804002333 Walker A motif; other site 399804002334 ATP binding site [chemical binding]; other site 399804002335 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 399804002336 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 399804002337 Walker A motif; other site 399804002338 ATP binding site [chemical binding]; other site 399804002339 Walker B motif; other site 399804002340 arginine finger; other site 399804002341 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 399804002342 MPN+ (JAMM) motif; other site 399804002343 Zinc-binding site [ion binding]; other site 399804002344 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 399804002345 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 399804002346 Domain of unknown function (DUF1508); Region: DUF1508; pfam07411 399804002347 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804002348 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804002349 dimer interface [polypeptide binding]; other site 399804002350 putative CheW interface [polypeptide binding]; other site 399804002351 Hemerythrin; Region: Hemerythrin; cd12107 399804002352 Fe binding site [ion binding]; other site 399804002353 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 399804002354 Superinfection exclusion protein B; Region: SieB; pfam14163 399804002355 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 399804002356 ATP binding site [chemical binding]; other site 399804002357 Mg2+ binding site [ion binding]; other site 399804002358 G-X-G motif; other site 399804002359 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 399804002360 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 399804002361 putative ATP binding site [chemical binding]; other site 399804002362 putative substrate interface [chemical binding]; other site 399804002363 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 399804002364 eyelet of channel; other site 399804002365 trimer interface [polypeptide binding]; other site 399804002366 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 399804002367 epoxyqueuosine reductase; Region: TIGR00276 399804002368 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 399804002369 Protein of unknown function (DUF3069); Region: DUF3069; pfam11269 399804002370 malate dehydrogenase; Provisional; Region: PRK13529 399804002371 Malic enzyme, N-terminal domain; Region: malic; pfam00390 399804002372 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 399804002373 NAD(P) binding site [chemical binding]; other site 399804002374 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 399804002375 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 399804002376 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 399804002377 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 399804002378 Bacterial PH domain; Region: DUF304; pfam03703 399804002379 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 399804002380 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 399804002381 synthetase active site [active] 399804002382 NTP binding site [chemical binding]; other site 399804002383 metal binding site [ion binding]; metal-binding site 399804002384 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 399804002385 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 399804002386 active site 399804002387 Zn binding site [ion binding]; other site 399804002388 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 399804002389 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 399804002390 RNA binding surface [nucleotide binding]; other site 399804002391 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 399804002392 active site 399804002393 uracil binding [chemical binding]; other site 399804002394 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 399804002395 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 399804002396 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 399804002397 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 399804002398 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 399804002399 DNA binding residues [nucleotide binding] 399804002400 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804002401 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 399804002402 dimerization interface [polypeptide binding]; other site 399804002403 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804002404 dimer interface [polypeptide binding]; other site 399804002405 putative CheW interface [polypeptide binding]; other site 399804002406 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 399804002407 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 399804002408 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 399804002409 active site 399804002410 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 399804002411 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 399804002412 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 399804002413 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 399804002414 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 399804002415 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 399804002416 tRNA; other site 399804002417 putative tRNA binding site [nucleotide binding]; other site 399804002418 putative NADP binding site [chemical binding]; other site 399804002419 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 399804002420 peptide chain release factor 1; Validated; Region: prfA; PRK00591 399804002421 This domain is found in peptide chain release factors; Region: PCRF; smart00937 399804002422 RF-1 domain; Region: RF-1; pfam00472 399804002423 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 399804002424 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 399804002425 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 399804002426 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 399804002427 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 399804002428 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 399804002429 Tetratricopeptide repeat; Region: TPR_9; pfam13371 399804002430 Protein of unknown function (DUF819); Region: DUF819; cl02317 399804002431 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 399804002432 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 399804002433 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 399804002434 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 399804002435 heme-binding residues [chemical binding]; other site 399804002436 L-aspartate oxidase; Provisional; Region: PRK06175 399804002437 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 399804002438 Gram-negative porin; Region: Porin_4; pfam13609 399804002439 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 399804002440 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804002441 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 399804002442 dimerization interface [polypeptide binding]; other site 399804002443 Protein of unknown function (DUF819); Region: DUF819; cl02317 399804002444 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 399804002445 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 399804002446 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 399804002447 Nitrogen regulatory protein P-II; Region: P-II; smart00938 399804002448 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 399804002449 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 399804002450 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 399804002451 Predicted integral membrane protein [Function unknown]; Region: COG5652 399804002452 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 399804002453 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 399804002454 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 399804002455 muropeptide transporter; Reviewed; Region: ampG; PRK11902 399804002456 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 399804002457 putative substrate translocation pore; other site 399804002458 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 399804002459 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 399804002460 substrate binding site [chemical binding]; other site 399804002461 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 399804002462 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 399804002463 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 399804002464 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 399804002465 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 399804002466 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 399804002467 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 399804002468 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 399804002469 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 399804002470 aromatic acid decarboxylase; Validated; Region: PRK05920 399804002471 Flavoprotein; Region: Flavoprotein; pfam02441 399804002472 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 399804002473 active site 399804002474 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 399804002475 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 399804002476 Walker A/P-loop; other site 399804002477 ATP binding site [chemical binding]; other site 399804002478 Q-loop/lid; other site 399804002479 ABC transporter signature motif; other site 399804002480 Walker B; other site 399804002481 D-loop; other site 399804002482 H-loop/switch region; other site 399804002483 inner membrane transport permease; Provisional; Region: PRK15066 399804002484 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 399804002485 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 399804002486 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 399804002487 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 399804002488 catalytic residues [active] 399804002489 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined; Region: PA_subtilisin_1; cd04818 399804002490 PA/protease or protease-like domain interface [polypeptide binding]; other site 399804002491 Peptidase S8 family domain in Vpr-like proteins; Region: Peptidases_S8_subtilisin_Vpr-like; cd07474 399804002492 Fn3-like domain (DUF1034); Region: DUF1034; pfam06280 399804002493 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 399804002494 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 399804002495 putative DNA binding site [nucleotide binding]; other site 399804002496 putative Zn2+ binding site [ion binding]; other site 399804002497 AsnC family; Region: AsnC_trans_reg; pfam01037 399804002498 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 399804002499 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 399804002500 active site 399804002501 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 399804002502 Peptidase family U32; Region: Peptidase_U32; pfam01136 399804002503 Collagenase; Region: DUF3656; pfam12392 399804002504 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804002505 Protein of unknown function (DUF2004); Region: DUF2004; pfam09406 399804002506 Cupin domain; Region: Cupin_2; cl17218 399804002507 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 399804002508 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 399804002509 active site 399804002510 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 399804002511 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 399804002512 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 399804002513 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 399804002514 catalytic residue [active] 399804002515 MltA-interacting protein MipA; Region: MipA; cl01504 399804002516 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 399804002517 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804002518 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 399804002519 active site 399804002520 phosphorylation site [posttranslational modification] 399804002521 intermolecular recognition site; other site 399804002522 dimerization interface [polypeptide binding]; other site 399804002523 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 399804002524 DNA binding site [nucleotide binding] 399804002525 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804002526 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 399804002527 dimerization interface [polypeptide binding]; other site 399804002528 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 399804002529 dimer interface [polypeptide binding]; other site 399804002530 phosphorylation site [posttranslational modification] 399804002531 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 399804002532 ATP binding site [chemical binding]; other site 399804002533 Mg2+ binding site [ion binding]; other site 399804002534 G-X-G motif; other site 399804002535 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 399804002536 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 399804002537 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 399804002538 active site 399804002539 catalytic tetrad [active] 399804002540 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 399804002541 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 399804002542 E3 interaction surface; other site 399804002543 lipoyl attachment site [posttranslational modification]; other site 399804002544 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 399804002545 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 399804002546 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 399804002547 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 399804002548 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 399804002549 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 399804002550 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 399804002551 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 399804002552 catalytic loop [active] 399804002553 iron binding site [ion binding]; other site 399804002554 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 399804002555 FAD binding pocket [chemical binding]; other site 399804002556 FAD binding motif [chemical binding]; other site 399804002557 phosphate binding motif [ion binding]; other site 399804002558 beta-alpha-beta structure motif; other site 399804002559 NAD binding pocket [chemical binding]; other site 399804002560 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 399804002561 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 399804002562 Beta-lactamase; Region: Beta-lactamase; pfam00144 399804002563 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 399804002564 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 399804002565 MarR family; Region: MarR; pfam01047 399804002566 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 399804002567 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804002568 Coenzyme A binding pocket [chemical binding]; other site 399804002569 inosine/xanthosine triphosphatase; Reviewed; Region: PRK05074 399804002570 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 399804002571 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 399804002572 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 399804002573 active site 399804002574 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 399804002575 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 399804002576 serine transporter; Region: stp; TIGR00814 399804002577 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 399804002578 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804002579 Coenzyme A binding pocket [chemical binding]; other site 399804002580 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 399804002581 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 399804002582 META domain; Region: META; pfam03724 399804002583 S-adenosylmethionine synthetase; Validated; Region: PRK05250 399804002584 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 399804002585 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 399804002586 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 399804002587 transketolase; Reviewed; Region: PRK12753 399804002588 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 399804002589 TPP-binding site [chemical binding]; other site 399804002590 dimer interface [polypeptide binding]; other site 399804002591 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 399804002592 PYR/PP interface [polypeptide binding]; other site 399804002593 dimer interface [polypeptide binding]; other site 399804002594 TPP binding site [chemical binding]; other site 399804002595 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 399804002596 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 399804002597 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 399804002598 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 399804002599 Phosphoglycerate kinase; Region: PGK; pfam00162 399804002600 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 399804002601 substrate binding site [chemical binding]; other site 399804002602 hinge regions; other site 399804002603 ADP binding site [chemical binding]; other site 399804002604 catalytic site [active] 399804002605 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 399804002606 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 399804002607 intersubunit interface [polypeptide binding]; other site 399804002608 active site 399804002609 zinc binding site [ion binding]; other site 399804002610 Na+ binding site [ion binding]; other site 399804002611 Protein of unknown function, DUF481; Region: DUF481; pfam04338 399804002612 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 399804002613 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 399804002614 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 399804002615 DNA binding site [nucleotide binding] 399804002616 PAS domain; Region: PAS_9; pfam13426 399804002617 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804002618 radical SAM protein, TatD family-associated; Region: tatD_link_rSAM; TIGR04038 399804002619 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 399804002620 FeS/SAM binding site; other site 399804002621 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804002622 Protein export membrane protein; Region: SecD_SecF; cl14618 399804002623 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804002624 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804002625 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 399804002626 DEAD-like helicases superfamily; Region: DEXDc; smart00487 399804002627 ATP binding site [chemical binding]; other site 399804002628 Mg++ binding site [ion binding]; other site 399804002629 motif III; other site 399804002630 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 399804002631 nucleotide binding region [chemical binding]; other site 399804002632 ATP-binding site [chemical binding]; other site 399804002633 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 399804002634 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 399804002635 S-adenosylmethionine binding site [chemical binding]; other site 399804002636 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 399804002637 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 399804002638 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 399804002639 active site 399804002640 Int/Topo IB signature motif; other site 399804002641 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 399804002642 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804002643 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 399804002644 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 399804002645 DHH family; Region: DHH; pfam01368 399804002646 DHHA1 domain; Region: DHHA1; pfam02272 399804002647 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804002648 Coenzyme A binding pocket [chemical binding]; other site 399804002649 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 399804002650 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 399804002651 catalytic residue [active] 399804002652 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 399804002653 catalytic residues [active] 399804002654 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 399804002655 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 399804002656 peroxiredoxin; Region: AhpC; TIGR03137 399804002657 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 399804002658 dimer interface [polypeptide binding]; other site 399804002659 decamer (pentamer of dimers) interface [polypeptide binding]; other site 399804002660 catalytic triad [active] 399804002661 peroxidatic and resolving cysteines [active] 399804002662 multifunctional aminopeptidase A; Provisional; Region: PRK00913 399804002663 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 399804002664 interface (dimer of trimers) [polypeptide binding]; other site 399804002665 Substrate-binding/catalytic site; other site 399804002666 Zn-binding sites [ion binding]; other site 399804002667 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 399804002668 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 399804002669 Mechanosensitive ion channel; Region: MS_channel; pfam00924 399804002670 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 399804002671 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 399804002672 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 399804002673 putative ligand binding site [chemical binding]; other site 399804002674 putative NAD binding site [chemical binding]; other site 399804002675 catalytic site [active] 399804002676 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 399804002677 heme-binding residues [chemical binding]; other site 399804002678 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 399804002679 L-aspartate oxidase; Provisional; Region: PRK06175 399804002680 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 399804002681 S-adenosylmethionine binding site [chemical binding]; other site 399804002682 Rhomboid family; Region: Rhomboid; pfam01694 399804002683 calcium/sodium:proton antiporter; Provisional; Region: PRK10599 399804002684 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 399804002685 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804002686 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804002687 Predicted membrane protein [Function unknown]; Region: COG2119 399804002688 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 399804002689 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 399804002690 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 399804002691 Peptidase S46; Region: Peptidase_S46; pfam10459 399804002692 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 399804002693 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 399804002694 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 399804002695 RNA binding surface [nucleotide binding]; other site 399804002696 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 399804002697 probable active site [active] 399804002698 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 399804002699 H+/citrate symporter [Energy production and conversion]; Region: CitM; cl17620 399804002700 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804002701 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 399804002702 dimerization interface [polypeptide binding]; other site 399804002703 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804002704 dimer interface [polypeptide binding]; other site 399804002705 putative CheW interface [polypeptide binding]; other site 399804002706 EamA-like transporter family; Region: EamA; pfam00892 399804002707 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 399804002708 Helix-turn-helix domain; Region: HTH_18; pfam12833 399804002709 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 399804002710 Protein of unknown function (DUF2474); Region: DUF2474; pfam10617 399804002711 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 399804002712 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 399804002713 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 399804002714 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 399804002715 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804002716 DNA-binding site [nucleotide binding]; DNA binding site 399804002717 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 399804002718 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804002719 homodimer interface [polypeptide binding]; other site 399804002720 catalytic residue [active] 399804002721 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 399804002722 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 399804002723 homodimer interface [polypeptide binding]; other site 399804002724 substrate-cofactor binding pocket; other site 399804002725 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804002726 catalytic residue [active] 399804002727 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 399804002728 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 399804002729 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 399804002730 S-adenosylmethionine binding site [chemical binding]; other site 399804002731 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; pfam13532 399804002732 BolA-like protein; Region: BolA; cl00386 399804002733 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 399804002734 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 399804002735 S-ribosylhomocysteinase; Provisional; Region: PRK02260 399804002736 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 399804002737 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804002738 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 399804002739 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 399804002740 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 399804002741 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 399804002742 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 399804002743 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 399804002744 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 399804002745 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 399804002746 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 399804002747 FAD binding pocket [chemical binding]; other site 399804002748 FAD binding motif [chemical binding]; other site 399804002749 phosphate binding motif [ion binding]; other site 399804002750 beta-alpha-beta structure motif; other site 399804002751 NAD binding pocket [chemical binding]; other site 399804002752 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 399804002753 ApbE family; Region: ApbE; pfam02424 399804002754 Protein of unknown function (DUF539); Region: DUF539; cl01129 399804002755 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 399804002756 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 399804002757 heme binding site [chemical binding]; other site 399804002758 ferroxidase pore; other site 399804002759 ferroxidase diiron center [ion binding]; other site 399804002760 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 399804002761 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 399804002762 heme binding site [chemical binding]; other site 399804002763 ferroxidase pore; other site 399804002764 ferroxidase diiron center [ion binding]; other site 399804002765 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804002766 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 399804002767 dimerization interface [polypeptide binding]; other site 399804002768 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804002769 dimer interface [polypeptide binding]; other site 399804002770 putative CheW interface [polypeptide binding]; other site 399804002771 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 399804002772 active site 399804002773 DNA polymerase IV; Validated; Region: PRK02406 399804002774 DNA binding site [nucleotide binding] 399804002775 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804002776 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804002777 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 399804002778 putative effector binding pocket; other site 399804002779 dimerization interface [polypeptide binding]; other site 399804002780 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 399804002781 EamA-like transporter family; Region: EamA; pfam00892 399804002782 EamA-like transporter family; Region: EamA; pfam00892 399804002783 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804002784 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 399804002785 dimerization interface [polypeptide binding]; other site 399804002786 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804002787 dimer interface [polypeptide binding]; other site 399804002788 putative CheW interface [polypeptide binding]; other site 399804002789 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 399804002790 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 399804002791 metal binding site [ion binding]; metal-binding site 399804002792 dimer interface [polypeptide binding]; other site 399804002793 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 399804002794 interface (dimer of trimers) [polypeptide binding]; other site 399804002795 Substrate-binding/catalytic site; other site 399804002796 Zn-binding sites [ion binding]; other site 399804002797 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 399804002798 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 399804002799 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 399804002800 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 399804002801 Walker A/P-loop; other site 399804002802 ATP binding site [chemical binding]; other site 399804002803 Q-loop/lid; other site 399804002804 ABC transporter signature motif; other site 399804002805 Walker B; other site 399804002806 D-loop; other site 399804002807 H-loop/switch region; other site 399804002808 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 399804002809 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 399804002810 ABC-ATPase subunit interface; other site 399804002811 dimer interface [polypeptide binding]; other site 399804002812 putative PBP binding regions; other site 399804002813 Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a...; Region: HutB; cd01149 399804002814 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 399804002815 putative hemin binding site; other site 399804002816 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 399804002817 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 399804002818 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 399804002819 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 399804002820 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 399804002821 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 399804002822 N-terminal plug; other site 399804002823 ligand-binding site [chemical binding]; other site 399804002824 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 399804002825 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 399804002826 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 399804002827 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 399804002828 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 399804002829 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804002830 Walker A/P-loop; other site 399804002831 ATP binding site [chemical binding]; other site 399804002832 Q-loop/lid; other site 399804002833 ABC transporter signature motif; other site 399804002834 Walker B; other site 399804002835 D-loop; other site 399804002836 H-loop/switch region; other site 399804002837 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05677 399804002838 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 399804002839 acyl-activating enzyme (AAE) consensus motif; other site 399804002840 putative AMP binding site [chemical binding]; other site 399804002841 putative active site [active] 399804002842 putative CoA binding site [chemical binding]; other site 399804002843 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 399804002844 4Fe-4S binding domain; Region: Fer4_5; pfam12801 399804002845 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 399804002846 PAS domain S-box; Region: sensory_box; TIGR00229 399804002847 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 399804002848 putative active site [active] 399804002849 heme pocket [chemical binding]; other site 399804002850 phage shock protein operon transcriptional activator; Provisional; Region: pspF; PRK11608 399804002851 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 399804002852 Walker A motif; other site 399804002853 ATP binding site [chemical binding]; other site 399804002854 Walker B motif; other site 399804002855 arginine finger; other site 399804002856 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804002857 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 399804002858 DsbD alpha interface [polypeptide binding]; other site 399804002859 catalytic residues [active] 399804002860 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 399804002861 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 399804002862 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 399804002863 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 399804002864 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 399804002865 ligand binding site [chemical binding]; other site 399804002866 active site 399804002867 UGI interface [polypeptide binding]; other site 399804002868 catalytic site [active] 399804002869 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 399804002870 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 399804002871 substrate binding pocket [chemical binding]; other site 399804002872 chain length determination region; other site 399804002873 substrate-Mg2+ binding site; other site 399804002874 catalytic residues [active] 399804002875 aspartate-rich region 1; other site 399804002876 active site lid residues [active] 399804002877 aspartate-rich region 2; other site 399804002878 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 399804002879 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 399804002880 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 399804002881 GTPase CgtA; Reviewed; Region: obgE; PRK12298 399804002882 GTP1/OBG; Region: GTP1_OBG; pfam01018 399804002883 Obg GTPase; Region: Obg; cd01898 399804002884 G1 box; other site 399804002885 GTP/Mg2+ binding site [chemical binding]; other site 399804002886 Switch I region; other site 399804002887 G2 box; other site 399804002888 G3 box; other site 399804002889 Switch II region; other site 399804002890 G4 box; other site 399804002891 G5 box; other site 399804002892 Uncharacterized conserved protein [Function unknown]; Region: COG2966 399804002893 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 399804002894 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 399804002895 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 399804002896 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 399804002897 NADP+ binding site [chemical binding]; other site 399804002898 folate binding site [chemical binding]; other site 399804002899 Protein of unknown function (DUF3718); Region: DUF3718; pfam12514 399804002900 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 399804002901 dimerization interface [polypeptide binding]; other site 399804002902 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804002903 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804002904 dimer interface [polypeptide binding]; other site 399804002905 putative CheW interface [polypeptide binding]; other site 399804002906 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 399804002907 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 399804002908 active site 399804002909 metal binding site [ion binding]; metal-binding site 399804002910 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 399804002911 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 399804002912 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 399804002913 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 399804002914 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 399804002915 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 399804002916 SurA N-terminal domain; Region: SurA_N; pfam09312 399804002917 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 399804002918 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 399804002919 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 399804002920 OstA-like protein; Region: OstA; cl00844 399804002921 Organic solvent tolerance protein; Region: OstA_C; pfam04453 399804002922 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 399804002923 Phosphotransferase enzyme family; Region: APH; pfam01636 399804002924 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 399804002925 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 399804002926 Substrate binding site; other site 399804002927 metal-binding site 399804002928 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 399804002929 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 399804002930 putative metal binding site [ion binding]; other site 399804002931 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 399804002932 HSP70 interaction site [polypeptide binding]; other site 399804002933 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 399804002934 glycerate dehydrogenase; Provisional; Region: PRK06487 399804002935 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 399804002936 putative ligand binding site [chemical binding]; other site 399804002937 putative NAD binding site [chemical binding]; other site 399804002938 catalytic site [active] 399804002939 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 399804002940 binding surface 399804002941 TPR motif; other site 399804002942 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 399804002943 Protein of unknown function (DUF3142); Region: DUF3142; pfam11340 399804002944 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 399804002945 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 399804002946 active site 399804002947 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 399804002948 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804002949 ATP-grasp domain; Region: ATP-grasp; pfam02222 399804002950 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 399804002951 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 399804002952 Walker A/P-loop; other site 399804002953 ATP binding site [chemical binding]; other site 399804002954 Q-loop/lid; other site 399804002955 ABC transporter signature motif; other site 399804002956 Walker B; other site 399804002957 D-loop; other site 399804002958 H-loop/switch region; other site 399804002959 TOBE-like domain; Region: TOBE_3; pfam12857 399804002960 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 399804002961 dimer interface [polypeptide binding]; other site 399804002962 conserved gate region; other site 399804002963 putative PBP binding loops; other site 399804002964 ABC-ATPase subunit interface; other site 399804002965 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 399804002966 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 399804002967 dimer interface [polypeptide binding]; other site 399804002968 conserved gate region; other site 399804002969 putative PBP binding loops; other site 399804002970 ABC-ATPase subunit interface; other site 399804002971 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CysP; COG4150 399804002972 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 399804002973 cysteine synthase B; Region: cysM; TIGR01138 399804002974 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 399804002975 dimer interface [polypeptide binding]; other site 399804002976 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804002977 catalytic residue [active] 399804002978 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 399804002979 Predicted Fe-S protein [General function prediction only]; Region: COG3313 399804002980 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804002981 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 399804002982 dimer interface [polypeptide binding]; other site 399804002983 phosphorylation site [posttranslational modification] 399804002984 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 399804002985 ATP binding site [chemical binding]; other site 399804002986 Mg2+ binding site [ion binding]; other site 399804002987 G-X-G motif; other site 399804002988 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 399804002989 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 399804002990 active site 399804002991 phosphorylation site [posttranslational modification] 399804002992 intermolecular recognition site; other site 399804002993 dimerization interface [polypeptide binding]; other site 399804002994 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 399804002995 DNA binding site [nucleotide binding] 399804002996 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 399804002997 MltA-interacting protein MipA; Region: MipA; cl01504 399804002998 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 399804002999 YcxB-like protein; Region: YcxB; pfam14317 399804003000 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 399804003001 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 399804003002 active site 399804003003 metal binding site [ion binding]; metal-binding site 399804003004 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 399804003005 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 399804003006 Predicted transcriptional regulator [Transcription]; Region: COG2345 399804003007 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 399804003008 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 399804003009 RNA binding surface [nucleotide binding]; other site 399804003010 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 399804003011 active site 399804003012 uracil binding [chemical binding]; other site 399804003013 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 399804003014 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804003015 dimer interface [polypeptide binding]; other site 399804003016 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 399804003017 putative CheW interface [polypeptide binding]; other site 399804003018 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 399804003019 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 399804003020 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 399804003021 RNA binding surface [nucleotide binding]; other site 399804003022 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 399804003023 active site 399804003024 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 399804003025 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 399804003026 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 399804003027 Clp amino terminal domain; Region: Clp_N; pfam02861 399804003028 Clp amino terminal domain; Region: Clp_N; pfam02861 399804003029 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 399804003030 Walker A motif; other site 399804003031 ATP binding site [chemical binding]; other site 399804003032 Walker B motif; other site 399804003033 arginine finger; other site 399804003034 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 399804003035 Walker A motif; other site 399804003036 ATP binding site [chemical binding]; other site 399804003037 Walker B motif; other site 399804003038 arginine finger; other site 399804003039 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 399804003040 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 399804003041 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 399804003042 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 399804003043 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; pfam04277 399804003044 oxaloacetate decarboxylase; Provisional; Region: PRK14040 399804003045 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 399804003046 active site 399804003047 catalytic residues [active] 399804003048 metal binding site [ion binding]; metal-binding site 399804003049 homodimer binding site [polypeptide binding]; other site 399804003050 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 399804003051 carboxyltransferase (CT) interaction site; other site 399804003052 biotinylation site [posttranslational modification]; other site 399804003053 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 399804003054 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 399804003055 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 399804003056 Predicted membrane protein [Function unknown]; Region: COG1238 399804003057 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 399804003058 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 399804003059 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 399804003060 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 399804003061 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 399804003062 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 399804003063 glutamate--cysteine ligase; Provisional; Region: PRK02107 399804003064 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 399804003065 N-acetyl-D-glucosamine binding site [chemical binding]; other site 399804003066 catalytic residue [active] 399804003067 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 399804003068 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 399804003069 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804003070 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804003071 metal binding site [ion binding]; metal-binding site 399804003072 active site 399804003073 I-site; other site 399804003074 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 399804003075 ATP-grasp domain; Region: ATP-grasp; pfam02222 399804003076 AIR carboxylase; Region: AIRC; pfam00731 399804003077 putative transporter; Provisional; Region: PRK11660 399804003078 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 399804003079 Sulfate transporter family; Region: Sulfate_transp; pfam00916 399804003080 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 399804003081 von Willebrand factor; Region: vWF_A; pfam12450 399804003082 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 399804003083 VWA subgroup: 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_subgroup; cd01465 399804003084 metal ion-dependent adhesion site (MIDAS); other site 399804003085 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 399804003086 RNA polymerase sigma factor; Provisional; Region: PRK12513 399804003087 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 399804003088 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cl17257 399804003089 DNA binding residues [nucleotide binding] 399804003090 Hemerythrin-like domain; Region: Hr-like; cd12108 399804003091 Fe binding site [ion binding]; other site 399804003092 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 399804003093 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 399804003094 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 399804003095 active site 399804003096 dimer interface [polypeptide binding]; other site 399804003097 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 399804003098 dimer interface [polypeptide binding]; other site 399804003099 active site 399804003100 transaldolase-like protein; Provisional; Region: PTZ00411 399804003101 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 399804003102 active site 399804003103 dimer interface [polypeptide binding]; other site 399804003104 catalytic residue [active] 399804003105 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 399804003106 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804003107 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 399804003108 ligand binding site [chemical binding]; other site 399804003109 putative phosphoketolase; Provisional; Region: PRK05261 399804003110 Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent...; Region: TPP_PK; cd02011 399804003111 TPP-binding site; other site 399804003112 XFP C-terminal domain; Region: XFP_C; pfam09363 399804003113 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 399804003114 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 399804003115 hypothetical protein; Validated; Region: PRK02101 399804003116 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 399804003117 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions; Region: PA_M28_2; cd04815 399804003118 PA/protease or protease-like domain interface [polypeptide binding]; other site 399804003119 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 399804003120 Peptidase family M28; Region: Peptidase_M28; pfam04389 399804003121 metal binding site [ion binding]; metal-binding site 399804003122 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 399804003123 dimerization interface [polypeptide binding]; other site 399804003124 putative DNA binding site [nucleotide binding]; other site 399804003125 putative Zn2+ binding site [ion binding]; other site 399804003126 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 399804003127 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 399804003128 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 399804003129 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 399804003130 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 399804003131 active site 399804003132 Riboflavin kinase; Region: Flavokinase; smart00904 399804003133 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 399804003134 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 399804003135 HIGH motif; other site 399804003136 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 399804003137 active site 399804003138 KMSKS motif; other site 399804003139 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 399804003140 tRNA binding surface [nucleotide binding]; other site 399804003141 anticodon binding site; other site 399804003142 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 399804003143 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 399804003144 lipoprotein signal peptidase; Provisional; Region: PRK14787 399804003145 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 399804003146 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804003147 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 399804003148 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 399804003149 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 399804003150 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 399804003151 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 399804003152 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 399804003153 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 399804003154 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 399804003155 Type II transport protein GspH; Region: GspH; pfam12019 399804003156 Type II transport protein GspH; Region: GspH; pfam12019 399804003157 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 399804003158 Nitrogen regulatory protein P-II; Region: P-II; smart00938 399804003159 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 399804003160 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 399804003161 Transcriptional regulators [Transcription]; Region: PurR; COG1609 399804003162 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 399804003163 DNA binding site [nucleotide binding] 399804003164 domain linker motif; other site 399804003165 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 399804003166 putative ligand binding site [chemical binding]; other site 399804003167 putative dimerization interface [polypeptide binding]; other site 399804003168 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 399804003169 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 399804003170 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 399804003171 Putative carbohydrate binding domain; Region: CHB_HEX; smart01081 399804003172 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 399804003173 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 399804003174 active site 399804003175 C-terminal Early set domain associated with the catalytic domain of chitobiase (also called N-acetylglucosaminidase); Region: E_set_Chitobiase_C; cd02847 399804003176 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 399804003177 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 399804003178 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 399804003179 dimer interface [polypeptide binding]; other site 399804003180 active site 399804003181 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 399804003182 dimer interface [polypeptide binding]; other site 399804003183 active site 399804003184 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 399804003185 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 399804003186 active site 399804003187 dimer interface [polypeptide binding]; other site 399804003188 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 399804003189 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 399804003190 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 399804003191 putative substrate translocation pore; other site 399804003192 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 399804003193 Predicted enzyme of the cupin superfamily [General function prediction only]; Region: COG3450 399804003194 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 399804003195 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 399804003196 tetrameric interface [polypeptide binding]; other site 399804003197 NAD binding site [chemical binding]; other site 399804003198 catalytic residues [active] 399804003199 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 399804003200 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 399804003201 inhibitor-cofactor binding pocket; inhibition site 399804003202 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804003203 catalytic residue [active] 399804003204 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 399804003205 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 399804003206 NAD(P) binding site [chemical binding]; other site 399804003207 catalytic residues [active] 399804003208 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804003209 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804003210 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804003211 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 399804003212 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 399804003213 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 399804003214 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 399804003215 active site residue [active] 399804003216 Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the...; Region: Chelatase_Class_II; cl02784 399804003217 active site 399804003218 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 399804003219 active site residue [active] 399804003220 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 399804003221 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 399804003222 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 399804003223 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 399804003224 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 399804003225 non-specific DNA binding site [nucleotide binding]; other site 399804003226 salt bridge; other site 399804003227 sequence-specific DNA binding site [nucleotide binding]; other site 399804003228 Cupin domain; Region: Cupin_2; pfam07883 399804003229 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 399804003230 Homeodomain-like domain; Region: HTH_23; pfam13384 399804003231 Winged helix-turn helix; Region: HTH_33; pfam13592 399804003232 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804003233 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804003234 Peptidase C26; Region: Peptidase_C26; pfam07722 399804003235 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 399804003236 catalytic triad [active] 399804003237 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 399804003238 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 399804003239 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 399804003240 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 399804003241 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 399804003242 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804003243 Walker A/P-loop; other site 399804003244 ATP binding site [chemical binding]; other site 399804003245 Q-loop/lid; other site 399804003246 ABC transporter signature motif; other site 399804003247 Walker B; other site 399804003248 D-loop; other site 399804003249 H-loop/switch region; other site 399804003250 TOBE domain; Region: TOBE_2; pfam08402 399804003251 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 399804003252 dimer interface [polypeptide binding]; other site 399804003253 conserved gate region; other site 399804003254 putative PBP binding loops; other site 399804003255 ABC-ATPase subunit interface; other site 399804003256 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 399804003257 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 399804003258 dimer interface [polypeptide binding]; other site 399804003259 conserved gate region; other site 399804003260 putative PBP binding loops; other site 399804003261 ABC-ATPase subunit interface; other site 399804003262 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 399804003263 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 399804003264 succinate-semialdehyde dehydrogenase I; Provisional; Region: gabD; PRK11241 399804003265 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 399804003266 tetramerization interface [polypeptide binding]; other site 399804003267 NAD(P) binding site [chemical binding]; other site 399804003268 catalytic residues [active] 399804003269 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 399804003270 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 399804003271 inhibitor-cofactor binding pocket; inhibition site 399804003272 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804003273 catalytic residue [active] 399804003274 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 399804003275 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 399804003276 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 399804003277 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 399804003278 putative substrate translocation pore; other site 399804003279 POT family; Region: PTR2; cl17359 399804003280 Cache domain; Region: Cache_1; pfam02743 399804003281 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 399804003282 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804003283 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804003284 dimer interface [polypeptide binding]; other site 399804003285 putative CheW interface [polypeptide binding]; other site 399804003286 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 399804003287 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 399804003288 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 399804003289 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 399804003290 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 399804003291 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 399804003292 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 399804003293 DNA binding residues [nucleotide binding] 399804003294 DNA primase; Validated; Region: dnaG; PRK05667 399804003295 CHC2 zinc finger; Region: zf-CHC2; pfam01807 399804003296 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 399804003297 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 399804003298 active site 399804003299 metal binding site [ion binding]; metal-binding site 399804003300 interdomain interaction site; other site 399804003301 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 399804003302 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 399804003303 Yqey-like protein; Region: YqeY; pfam09424 399804003304 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 399804003305 UGMP family protein; Validated; Region: PRK09604 399804003306 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 399804003307 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 399804003308 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 399804003309 homooctamer interface [polypeptide binding]; other site 399804003310 active site 399804003311 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 399804003312 catalytic center binding site [active] 399804003313 ATP binding site [chemical binding]; other site 399804003314 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 399804003315 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 399804003316 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 399804003317 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 399804003318 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 399804003319 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 399804003320 active site 399804003321 NTP binding site [chemical binding]; other site 399804003322 metal binding triad [ion binding]; metal-binding site 399804003323 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 399804003324 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804003325 Zn2+ binding site [ion binding]; other site 399804003326 Mg2+ binding site [ion binding]; other site 399804003327 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 399804003328 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 399804003329 Walker A motif; other site 399804003330 ATP binding site [chemical binding]; other site 399804003331 Walker B motif; other site 399804003332 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 399804003333 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 399804003334 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 399804003335 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 399804003336 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 399804003337 inhibitor-cofactor binding pocket; inhibition site 399804003338 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804003339 catalytic residue [active] 399804003340 aspartate carbamoyltransferase; Provisional; Region: PRK08192 399804003341 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 399804003342 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 399804003343 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 399804003344 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 399804003345 Cl- selectivity filter; other site 399804003346 Cl- binding residues [ion binding]; other site 399804003347 pore gating glutamate residue; other site 399804003348 dimer interface [polypeptide binding]; other site 399804003349 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 399804003350 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 399804003351 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 399804003352 putative peptidase; Provisional; Region: PRK11649 399804003353 Opacity-associated protein A N-terminal motif; Region: OapA_N; pfam08525 399804003354 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 399804003355 Peptidase family M23; Region: Peptidase_M23; pfam01551 399804003356 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 399804003357 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 399804003358 active site 399804003359 HIGH motif; other site 399804003360 dimer interface [polypeptide binding]; other site 399804003361 KMSKS motif; other site 399804003362 S4 RNA-binding domain; Region: S4; smart00363 399804003363 SnoaL-like domain; Region: SnoaL_2; pfam12680 399804003364 hypothetical protein; Provisional; Region: PRK10578 399804003365 UPF0126 domain; Region: UPF0126; pfam03458 399804003366 UPF0126 domain; Region: UPF0126; pfam03458 399804003367 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 399804003368 Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]; Region: CbiB; COG1270 399804003369 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 399804003370 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 399804003371 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 399804003372 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 399804003373 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 399804003374 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 399804003375 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 399804003376 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 399804003377 active site 399804003378 dimer interface [polypeptide binding]; other site 399804003379 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 399804003380 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 399804003381 active site 399804003382 FMN binding site [chemical binding]; other site 399804003383 substrate binding site [chemical binding]; other site 399804003384 3Fe-4S cluster binding site [ion binding]; other site 399804003385 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 399804003386 domain interface; other site 399804003387 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 399804003388 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 399804003389 FeS/SAM binding site; other site 399804003390 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 399804003391 putative binding surface; other site 399804003392 active site 399804003393 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804003394 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804003395 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 399804003396 dimerization interface [polypeptide binding]; other site 399804003397 cyclase homology domain; Region: CHD; cd07302 399804003398 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 399804003399 nucleotidyl binding site; other site 399804003400 metal binding site [ion binding]; metal-binding site 399804003401 dimer interface [polypeptide binding]; other site 399804003402 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 399804003403 putative DNA-binding cleft [nucleotide binding]; other site 399804003404 putative DNA clevage site; other site 399804003405 molecular lever; other site 399804003406 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 399804003407 putative active site [active] 399804003408 Ap4A binding site [chemical binding]; other site 399804003409 nudix motif; other site 399804003410 putative metal binding site [ion binding]; other site 399804003411 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 399804003412 GAF domain; Region: GAF; pfam01590 399804003413 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 399804003414 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 399804003415 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 399804003416 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 399804003417 thymidylate synthase; Reviewed; Region: thyA; PRK01827 399804003418 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 399804003419 dimerization interface [polypeptide binding]; other site 399804003420 active site 399804003421 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09561 399804003422 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 399804003423 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804003424 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 399804003425 dimerization interface [polypeptide binding]; other site 399804003426 Uncharacterized conserved protein [Function unknown]; Region: COG2938 399804003427 L-aspartate oxidase; Provisional; Region: PRK09077 399804003428 L-aspartate oxidase; Provisional; Region: PRK06175 399804003429 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 399804003430 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 399804003431 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 399804003432 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 399804003433 DNA binding residues [nucleotide binding] 399804003434 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 399804003435 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 399804003436 anti-sigma E factor; Provisional; Region: rseB; PRK09455 399804003437 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 399804003438 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 399804003439 GTP-binding protein LepA; Provisional; Region: PRK05433 399804003440 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 399804003441 G1 box; other site 399804003442 putative GEF interaction site [polypeptide binding]; other site 399804003443 GTP/Mg2+ binding site [chemical binding]; other site 399804003444 Switch I region; other site 399804003445 G2 box; other site 399804003446 G3 box; other site 399804003447 Switch II region; other site 399804003448 G4 box; other site 399804003449 G5 box; other site 399804003450 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 399804003451 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 399804003452 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 399804003453 signal peptidase I; Provisional; Region: PRK10861 399804003454 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 399804003455 Catalytic site [active] 399804003456 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 399804003457 ribonuclease III; Reviewed; Region: rnc; PRK00102 399804003458 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 399804003459 dimerization interface [polypeptide binding]; other site 399804003460 active site 399804003461 metal binding site [ion binding]; metal-binding site 399804003462 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 399804003463 dsRNA binding site [nucleotide binding]; other site 399804003464 GTPase Era; Reviewed; Region: era; PRK00089 399804003465 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 399804003466 G1 box; other site 399804003467 GTP/Mg2+ binding site [chemical binding]; other site 399804003468 Switch I region; other site 399804003469 G2 box; other site 399804003470 Switch II region; other site 399804003471 G3 box; other site 399804003472 G4 box; other site 399804003473 G5 box; other site 399804003474 KH domain; Region: KH_2; pfam07650 399804003475 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 399804003476 Recombination protein O N terminal; Region: RecO_N; pfam11967 399804003477 Recombination protein O C terminal; Region: RecO_C; pfam02565 399804003478 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 399804003479 active site 399804003480 hydrophilic channel; other site 399804003481 dimerization interface [polypeptide binding]; other site 399804003482 catalytic residues [active] 399804003483 active site lid [active] 399804003484 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 399804003485 Protein of unknown function (DUF962); Region: DUF962; cl01879 399804003486 Domain of unknown function DUF21; Region: DUF21; pfam01595 399804003487 hypothetical protein; Provisional; Region: PRK11573 399804003488 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 399804003489 Transporter associated domain; Region: CorC_HlyC; smart01091 399804003490 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 399804003491 signal recognition particle protein; Provisional; Region: PRK10867 399804003492 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 399804003493 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 399804003494 P loop; other site 399804003495 GTP binding site [chemical binding]; other site 399804003496 Signal peptide binding domain; Region: SRP_SPB; pfam02978 399804003497 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 399804003498 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 399804003499 RimM N-terminal domain; Region: RimM; pfam01782 399804003500 PRC-barrel domain; Region: PRC; pfam05239 399804003501 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 399804003502 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 399804003503 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 399804003504 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 399804003505 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 399804003506 Chorismate mutase type II; Region: CM_2; cl00693 399804003507 prephenate dehydrogenase; Validated; Region: PRK08507 399804003508 hybrid cluster protein; Provisional; Region: PRK05290 399804003509 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 399804003510 ACS interaction site; other site 399804003511 CODH interaction site; other site 399804003512 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 399804003513 hybrid metal cluster; other site 399804003514 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 399804003515 HCP oxidoreductase, NADH-dependent; Provisional; Region: PRK10684 399804003516 FAD binding pocket [chemical binding]; other site 399804003517 FAD binding motif [chemical binding]; other site 399804003518 phosphate binding motif [ion binding]; other site 399804003519 beta-alpha-beta structure motif; other site 399804003520 NAD binding pocket [chemical binding]; other site 399804003521 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 399804003522 catalytic loop [active] 399804003523 iron binding site [ion binding]; other site 399804003524 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 399804003525 Chorismate mutase type II; Region: CM_2; cl00693 399804003526 Prephenate dehydratase; Region: PDT; pfam00800 399804003527 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 399804003528 putative L-Phe binding site [chemical binding]; other site 399804003529 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 399804003530 multifunctional aminopeptidase A; Provisional; Region: PRK00913 399804003531 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 399804003532 interface (dimer of trimers) [polypeptide binding]; other site 399804003533 Substrate-binding/catalytic site; other site 399804003534 Zn-binding sites [ion binding]; other site 399804003535 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 399804003536 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 399804003537 lipopolysaccharide ABC transporter permease; Provisional; Region: PRK15071 399804003538 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 399804003539 RDD family; Region: RDD; pfam06271 399804003540 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 399804003541 Protein of unknown function, DUF486; Region: DUF486; pfam04342 399804003542 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 399804003543 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804003544 Coenzyme A binding pocket [chemical binding]; other site 399804003545 Protein of unknown function (DUF1449); Region: DUF1449; pfam07290 399804003546 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 399804003547 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 399804003548 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 399804003549 hypothetical protein; Provisional; Region: PRK09898 399804003550 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 399804003551 putative oxidoreductase; Provisional; Region: PRK09849 399804003552 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 399804003553 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 399804003554 hypothetical protein; Provisional; Region: PRK09947 399804003555 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 399804003556 intracellular protease, PfpI family; Region: PfpI; TIGR01382 399804003557 conserved cys residue [active] 399804003558 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 399804003559 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 399804003560 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 399804003561 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 399804003562 ATP binding site [chemical binding]; other site 399804003563 Mg++ binding site [ion binding]; other site 399804003564 motif III; other site 399804003565 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 399804003566 nucleotide binding region [chemical binding]; other site 399804003567 ATP-binding site [chemical binding]; other site 399804003568 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 399804003569 PAS fold; Region: PAS_3; pfam08447 399804003570 putative active site [active] 399804003571 heme pocket [chemical binding]; other site 399804003572 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804003573 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804003574 dimer interface [polypeptide binding]; other site 399804003575 putative CheW interface [polypeptide binding]; other site 399804003576 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 399804003577 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 399804003578 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 399804003579 active site 399804003580 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 399804003581 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 399804003582 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 399804003583 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 399804003584 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804003585 Short chain fatty acids transporter [Lipid metabolism]; Region: AtoE; COG2031 399804003586 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 399804003587 Predicted membrane protein [Function unknown]; Region: COG2311 399804003588 Protein of unknown function (DUF418); Region: DUF418; cl12135 399804003589 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 399804003590 nucleoside/Zn binding site; other site 399804003591 dimer interface [polypeptide binding]; other site 399804003592 catalytic motif [active] 399804003593 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 399804003594 CoenzymeA binding site [chemical binding]; other site 399804003595 subunit interaction site [polypeptide binding]; other site 399804003596 PHB binding site; other site 399804003597 Domain of unknown function (DUF368); Region: DUF368; pfam04018 399804003598 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 399804003599 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 399804003600 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 399804003601 YheO-like PAS domain; Region: PAS_6; pfam08348 399804003602 HTH domain; Region: HTH_22; pfam13309 399804003603 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 399804003604 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 399804003605 dimerization interface [polypeptide binding]; other site 399804003606 putative DNA binding site [nucleotide binding]; other site 399804003607 putative Zn2+ binding site [ion binding]; other site 399804003608 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 399804003609 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 399804003610 ArsC family; Region: ArsC; pfam03960 399804003611 catalytic residues [active] 399804003612 arsenical pump membrane protein; Provisional; Region: PRK15445 399804003613 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 399804003614 transmembrane helices; other site 399804003615 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 399804003616 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 399804003617 P loop; other site 399804003618 Nucleotide binding site [chemical binding]; other site 399804003619 DTAP/Switch II; other site 399804003620 Switch I; other site 399804003621 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 399804003622 P loop; other site 399804003623 Nucleotide binding site [chemical binding]; other site 399804003624 DTAP/Switch II; other site 399804003625 Switch I; other site 399804003626 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 399804003627 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 399804003628 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 399804003629 molybdopterin cofactor binding site; other site 399804003630 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 399804003631 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 399804003632 putative molybdopterin cofactor binding site; other site 399804003633 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 399804003634 4Fe-4S binding domain; Region: Fer4; pfam00037 399804003635 Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily; Region: eu-GS; cl00170 399804003636 glutathione (GSH) binding pocket [chemical binding]; other site 399804003637 active site residues [active] 399804003638 ATP binding pocket [chemical binding]; other site 399804003639 magnesium binding site [ion binding]; other site 399804003640 glycine rich loop; other site 399804003641 alanine rich loop; other site 399804003642 Predicted permeases [General function prediction only]; Region: COG0701 399804003643 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 399804003644 dimerization interface [polypeptide binding]; other site 399804003645 putative DNA binding site [nucleotide binding]; other site 399804003646 putative Zn2+ binding site [ion binding]; other site 399804003647 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 399804003648 Low molecular weight phosphatase family; Region: LMWPc; cd00115 399804003649 active site 399804003650 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 399804003651 dimerization interface [polypeptide binding]; other site 399804003652 putative DNA binding site [nucleotide binding]; other site 399804003653 putative Zn2+ binding site [ion binding]; other site 399804003654 Predicted permeases [General function prediction only]; Region: COG0701 399804003655 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 399804003656 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 399804003657 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 399804003658 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 399804003659 Major Facilitator Superfamily; Region: MFS_1; pfam07690 399804003660 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 399804003661 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 399804003662 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 399804003663 Sulfate transporter family; Region: Sulfate_transp; pfam00916 399804003664 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 399804003665 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 399804003666 Ligand Binding Site [chemical binding]; other site 399804003667 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 399804003668 Ligand Binding Site [chemical binding]; other site 399804003669 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 399804003670 SmpB-tmRNA interface; other site 399804003671 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 399804003672 putative coenzyme Q binding site [chemical binding]; other site 399804003673 RnfH family Ubiquitin; Region: Ub-RnfH; cl17382 399804003674 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 399804003675 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 399804003676 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 399804003677 active site 399804003678 SAM binding site [chemical binding]; other site 399804003679 homodimer interface [polypeptide binding]; other site 399804003680 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804003681 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804003682 metal binding site [ion binding]; metal-binding site 399804003683 active site 399804003684 I-site; other site 399804003685 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 399804003686 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 399804003687 TrkA-N domain; Region: TrkA_N; pfam02254 399804003688 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 399804003689 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 399804003690 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 399804003691 malate synthase A; Region: malate_syn_A; TIGR01344 399804003692 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 399804003693 active site 399804003694 isocitrate lyase; Provisional; Region: PRK15063 399804003695 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 399804003696 tetramer interface [polypeptide binding]; other site 399804003697 active site 399804003698 Mg2+/Mn2+ binding site [ion binding]; other site 399804003699 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 399804003700 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 399804003701 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 399804003702 putative alcohol dehydrogenase; Provisional; Region: PRK09860 399804003703 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 399804003704 dimer interface [polypeptide binding]; other site 399804003705 active site 399804003706 metal binding site [ion binding]; metal-binding site 399804003707 Transcriptional regulators [Transcription]; Region: MarR; COG1846 399804003708 MarR family; Region: MarR; pfam01047 399804003709 MarR family; Region: MarR_2; cl17246 399804003710 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 399804003711 active site 399804003712 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 399804003713 glycogen branching enzyme; Provisional; Region: PRK05402 399804003714 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 399804003715 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 399804003716 active site 399804003717 catalytic site [active] 399804003718 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 399804003719 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 399804003720 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 399804003721 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 399804003722 active site 399804003723 catalytic site [active] 399804003724 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 399804003725 homodimer interface [polypeptide binding]; other site 399804003726 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 399804003727 active site pocket [active] 399804003728 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 399804003729 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 399804003730 ligand binding site; other site 399804003731 oligomer interface; other site 399804003732 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 399804003733 dimer interface [polypeptide binding]; other site 399804003734 N-terminal domain interface [polypeptide binding]; other site 399804003735 sulfate 1 binding site; other site 399804003736 glycogen synthase; Provisional; Region: glgA; PRK00654 399804003737 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 399804003738 ADP-binding pocket [chemical binding]; other site 399804003739 homodimer interface [polypeptide binding]; other site 399804003740 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 399804003741 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 399804003742 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 399804003743 putative active site [active] 399804003744 heme pocket [chemical binding]; other site 399804003745 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 399804003746 PAS domain; Region: PAS_9; pfam13426 399804003747 putative active site [active] 399804003748 heme pocket [chemical binding]; other site 399804003749 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804003750 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804003751 metal binding site [ion binding]; metal-binding site 399804003752 active site 399804003753 I-site; other site 399804003754 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 399804003755 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 399804003756 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 399804003757 ATP binding site [chemical binding]; other site 399804003758 Mg++ binding site [ion binding]; other site 399804003759 motif III; other site 399804003760 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 399804003761 nucleotide binding region [chemical binding]; other site 399804003762 ATP-binding site [chemical binding]; other site 399804003763 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 399804003764 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 399804003765 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 399804003766 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 399804003767 substrate binding pocket [chemical binding]; other site 399804003768 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804003769 membrane-bound complex binding site; other site 399804003770 hinge residues; other site 399804003771 Protein of unknown function (DUF3087); Region: DUF3087; pfam11286 399804003772 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 399804003773 Major Facilitator Superfamily; Region: MFS_1; pfam07690 399804003774 putative substrate translocation pore; other site 399804003775 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 399804003776 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 399804003777 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 399804003778 Putative esterase; Region: Esterase; pfam00756 399804003779 putative acetyltransferase YhhY; Provisional; Region: PRK10140 399804003780 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804003781 Coenzyme A binding pocket [chemical binding]; other site 399804003782 This domain is found at the N terminal of the mitochondrial ATPase BSC1. It encodes the import and intramitochondrial sorting for the protein; Region: BCS1_N; smart01024 399804003783 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 399804003784 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 399804003785 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 399804003786 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 399804003787 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 399804003788 Cysteine-rich domain; Region: CCG; pfam02754 399804003789 Cysteine-rich domain; Region: CCG; pfam02754 399804003790 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 399804003791 FAD binding domain; Region: FAD_binding_4; pfam01565 399804003792 4Fe-4S binding domain; Region: Fer4; pfam00037 399804003793 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 399804003794 L-lactate permease; Region: Lactate_perm; cl00701 399804003795 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 399804003796 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03378 399804003797 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 399804003798 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 399804003799 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 399804003800 dimer interface [polypeptide binding]; other site 399804003801 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 399804003802 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 399804003803 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 399804003804 TPP-binding site; other site 399804003805 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 399804003806 PYR/PP interface [polypeptide binding]; other site 399804003807 dimer interface [polypeptide binding]; other site 399804003808 TPP binding site [chemical binding]; other site 399804003809 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 399804003810 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 399804003811 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 399804003812 substrate binding pocket [chemical binding]; other site 399804003813 chain length determination region; other site 399804003814 substrate-Mg2+ binding site; other site 399804003815 catalytic residues [active] 399804003816 aspartate-rich region 1; other site 399804003817 active site lid residues [active] 399804003818 aspartate-rich region 2; other site 399804003819 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 399804003820 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 399804003821 flagellar motor protein PomA; Reviewed; Region: PRK08990 399804003822 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 399804003823 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 399804003824 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804003825 ligand binding site [chemical binding]; other site 399804003826 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 399804003827 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 399804003828 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 399804003829 Ligand Binding Site [chemical binding]; other site 399804003830 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 399804003831 active site residue [active] 399804003832 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 399804003833 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804003834 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 399804003835 dimerization interface [polypeptide binding]; other site 399804003836 substrate binding pocket [chemical binding]; other site 399804003837 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 399804003838 Protein of unknown function (DUF423); Region: DUF423; pfam04241 399804003839 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 399804003840 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 399804003841 isocitrate dehydrogenase; Provisional; Region: PRK08997 399804003842 tartrate dehydrogenase; Region: TTC; TIGR02089 399804003843 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 399804003844 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804003845 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 399804003846 flap endonuclease-like protein; Provisional; Region: PRK09482 399804003847 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 399804003848 active site 399804003849 metal binding site 1 [ion binding]; metal-binding site 399804003850 putative 5' ssDNA interaction site; other site 399804003851 metal binding site 3; metal-binding site 399804003852 metal binding site 2 [ion binding]; metal-binding site 399804003853 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 399804003854 putative DNA binding site [nucleotide binding]; other site 399804003855 putative metal binding site [ion binding]; other site 399804003856 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 399804003857 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 399804003858 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804003859 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804003860 metal binding site [ion binding]; metal-binding site 399804003861 active site 399804003862 I-site; other site 399804003863 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 399804003864 binding surface 399804003865 TPR motif; other site 399804003866 Tetratricopeptide repeat; Region: TPR_12; pfam13424 399804003867 Tetratricopeptide repeat; Region: TPR_12; pfam13424 399804003868 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 399804003869 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 399804003870 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 399804003871 protein binding site [polypeptide binding]; other site 399804003872 recombination associated protein; Reviewed; Region: rdgC; PRK00321 399804003873 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 399804003874 trimer interface [polypeptide binding]; other site 399804003875 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 399804003876 eyelet of channel; other site 399804003877 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 399804003878 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 399804003879 active site 399804003880 phosphorylation site [posttranslational modification] 399804003881 intermolecular recognition site; other site 399804003882 dimerization interface [polypeptide binding]; other site 399804003883 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 399804003884 DNA binding site [nucleotide binding] 399804003885 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 399804003886 phosphate regulon sensor protein; Provisional; Region: phoR; PRK11006 399804003887 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 399804003888 putative active site [active] 399804003889 heme pocket [chemical binding]; other site 399804003890 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 399804003891 dimer interface [polypeptide binding]; other site 399804003892 phosphorylation site [posttranslational modification] 399804003893 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 399804003894 ATP binding site [chemical binding]; other site 399804003895 Mg2+ binding site [ion binding]; other site 399804003896 G-X-G motif; other site 399804003897 PBP superfamily domain; Region: PBP_like_2; cl17296 399804003898 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 399804003899 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 399804003900 active site 399804003901 Zn binding site [ion binding]; other site 399804003902 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 399804003903 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 399804003904 catalytic residues [active] 399804003905 dimer interface [polypeptide binding]; other site 399804003906 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 399804003907 MgtE intracellular N domain; Region: MgtE_N; smart00924 399804003908 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 399804003909 Divalent cation transporter; Region: MgtE; cl00786 399804003910 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 399804003911 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804003912 Coenzyme A binding pocket [chemical binding]; other site 399804003913 YfaZ precursor; Region: YfaZ; pfam07437 399804003914 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 399804003915 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 399804003916 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 399804003917 S-adenosylmethionine binding site [chemical binding]; other site 399804003918 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 399804003919 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 399804003920 C-terminal domain interface [polypeptide binding]; other site 399804003921 GSH binding site (G-site) [chemical binding]; other site 399804003922 dimer interface [polypeptide binding]; other site 399804003923 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 399804003924 N-terminal domain interface [polypeptide binding]; other site 399804003925 putative dimer interface [polypeptide binding]; other site 399804003926 active site 399804003927 TIGR02453 family protein; Region: TIGR02453 399804003928 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 399804003929 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 399804003930 N-terminal plug; other site 399804003931 ligand-binding site [chemical binding]; other site 399804003932 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 399804003933 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 399804003934 PhnA protein; Region: PhnA; pfam03831 399804003935 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 399804003936 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 399804003937 putative substrate translocation pore; other site 399804003938 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 399804003939 MarR family; Region: MarR; pfam01047 399804003940 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 399804003941 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 399804003942 putative active site [active] 399804003943 Zn binding site [ion binding]; other site 399804003944 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 399804003945 dimerization interface [polypeptide binding]; other site 399804003946 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804003947 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804003948 dimer interface [polypeptide binding]; other site 399804003949 putative CheW interface [polypeptide binding]; other site 399804003950 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 399804003951 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 399804003952 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804003953 BON domain; Region: BON; pfam04972 399804003954 BON domain; Region: BON; pfam04972 399804003955 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 399804003956 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 399804003957 Walker A motif; other site 399804003958 ATP binding site [chemical binding]; other site 399804003959 Walker B motif; other site 399804003960 arginine finger; other site 399804003961 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804003962 hypothetical protein; Provisional; Region: PRK12361 399804003963 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 399804003964 active site 399804003965 catalytic residues [active] 399804003966 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 399804003967 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding...; Region: NPD_FabD; cd04742 399804003968 FMN binding site [chemical binding]; other site 399804003969 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 399804003970 substrate binding site [chemical binding]; other site 399804003971 putative catalytic residue [active] 399804003972 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 399804003973 3-oxoacyl-acyl carrier protein synthase; Provisional; Region: PTZ00050 399804003974 active site 399804003975 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 399804003976 active site 399804003977 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 399804003978 active site 2 [active] 399804003979 dimer interface [polypeptide binding]; other site 399804003980 active site 1 [active] 399804003981 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 399804003982 active site 1 [active] 399804003983 dimer interface [polypeptide binding]; other site 399804003984 active site 2 [active] 399804003985 Acyl transferase domain; Region: Acyl_transf_1; cl08282 399804003986 Homeodomain-like domain; Region: HTH_23; pfam13384 399804003987 Winged helix-turn helix; Region: HTH_29; pfam13551 399804003988 Winged helix-turn helix; Region: HTH_33; pfam13592 399804003989 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804003990 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804003991 Winged helix-turn helix; Region: HTH_29; pfam13551 399804003992 Homeodomain-like domain; Region: HTH_23; pfam13384 399804003993 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 399804003994 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 399804003995 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 399804003996 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 399804003997 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 399804003998 SecY interacting protein Syd; Provisional; Region: PRK04968 399804003999 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; pfam10071 399804004000 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 399804004001 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 399804004002 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 399804004003 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 399804004004 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 399804004005 tRNA pseudouridine synthase C; Region: DUF446; pfam04287 399804004006 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 399804004007 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 399804004008 probable active site [active] 399804004009 flavodoxin; Provisional; Region: PRK08105 399804004010 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 399804004011 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 399804004012 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 399804004013 active site turn [active] 399804004014 phosphorylation site [posttranslational modification] 399804004015 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 399804004016 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 399804004017 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 399804004018 putative active site [active] 399804004019 putative substrate binding site [chemical binding]; other site 399804004020 putative cosubstrate binding site; other site 399804004021 catalytic site [active] 399804004022 PAS domain; Region: PAS_9; pfam13426 399804004023 GAF domain; Region: GAF_2; pfam13185 399804004024 GAF domain; Region: GAF; pfam01590 399804004025 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 399804004026 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804004027 Zn2+ binding site [ion binding]; other site 399804004028 Mg2+ binding site [ion binding]; other site 399804004029 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 399804004030 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 399804004031 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 399804004032 trimer interface [polypeptide binding]; other site 399804004033 active site 399804004034 substrate binding site [chemical binding]; other site 399804004035 CoA binding site [chemical binding]; other site 399804004036 PII uridylyl-transferase; Provisional; Region: PRK05007 399804004037 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 399804004038 metal binding triad; other site 399804004039 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 399804004040 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 399804004041 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 399804004042 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 399804004043 active site 399804004044 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 399804004045 rRNA interaction site [nucleotide binding]; other site 399804004046 S8 interaction site; other site 399804004047 putative laminin-1 binding site; other site 399804004048 elongation factor Ts; Provisional; Region: tsf; PRK09377 399804004049 UBA/TS-N domain; Region: UBA; pfam00627 399804004050 Elongation factor TS; Region: EF_TS; pfam00889 399804004051 Elongation factor TS; Region: EF_TS; pfam00889 399804004052 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 399804004053 putative nucleotide binding site [chemical binding]; other site 399804004054 uridine monophosphate binding site [chemical binding]; other site 399804004055 homohexameric interface [polypeptide binding]; other site 399804004056 ribosome recycling factor; Reviewed; Region: frr; PRK00083 399804004057 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 399804004058 hinge region; other site 399804004059 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 399804004060 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; cd00475 399804004061 catalytic residue [active] 399804004062 putative FPP diphosphate binding site; other site 399804004063 putative FPP binding hydrophobic cleft; other site 399804004064 dimer interface [polypeptide binding]; other site 399804004065 putative IPP diphosphate binding site; other site 399804004066 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 399804004067 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 399804004068 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 399804004069 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 399804004070 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 399804004071 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 399804004072 zinc metallopeptidase RseP; Provisional; Region: PRK10779 399804004073 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 399804004074 active site 399804004075 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 399804004076 protein binding site [polypeptide binding]; other site 399804004077 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 399804004078 protein binding site [polypeptide binding]; other site 399804004079 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 399804004080 putative substrate binding region [chemical binding]; other site 399804004081 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 399804004082 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 399804004083 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 399804004084 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 399804004085 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 399804004086 Surface antigen; Region: Bac_surface_Ag; pfam01103 399804004087 periplasmic chaperone; Provisional; Region: PRK10780 399804004088 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 399804004089 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 399804004090 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 399804004091 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 399804004092 trimer interface [polypeptide binding]; other site 399804004093 active site 399804004094 UDP-GlcNAc binding site [chemical binding]; other site 399804004095 lipid binding site [chemical binding]; lipid-binding site 399804004096 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 399804004097 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 399804004098 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 399804004099 active site 399804004100 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 399804004101 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 399804004102 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 399804004103 RNA/DNA hybrid binding site [nucleotide binding]; other site 399804004104 active site 399804004105 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 399804004106 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 399804004107 putative active site [active] 399804004108 putative PHP Thumb interface [polypeptide binding]; other site 399804004109 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 399804004110 generic binding surface II; other site 399804004111 generic binding surface I; other site 399804004112 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 399804004113 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 399804004114 Ligand Binding Site [chemical binding]; other site 399804004115 TilS substrate binding domain; Region: TilS; pfam09179 399804004116 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 399804004117 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804004118 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804004119 metal binding site [ion binding]; metal-binding site 399804004120 active site 399804004121 I-site; other site 399804004122 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 399804004123 DNA-binding site [nucleotide binding]; DNA binding site 399804004124 RNA-binding motif; other site 399804004125 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 399804004126 SWIM zinc finger; Region: SWIM; pfam04434 399804004127 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 399804004128 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 399804004129 ATP binding site [chemical binding]; other site 399804004130 putative Mg++ binding site [ion binding]; other site 399804004131 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 399804004132 nucleotide binding region [chemical binding]; other site 399804004133 ATP-binding site [chemical binding]; other site 399804004134 putative hydrolase; Validated; Region: PRK09248 399804004135 Polymerase and Histidinol Phosphatase domain of Ycdx like; Region: PHP_HisPPase_Ycdx_like; cd07437 399804004136 active site 399804004137 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 399804004138 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 399804004139 active site 399804004140 fructokinase; Reviewed; Region: PRK09557 399804004141 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 399804004142 nucleotide binding site [chemical binding]; other site 399804004143 Uncharacterized conserved protein [Function unknown]; Region: COG1434 399804004144 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 399804004145 putative active site [active] 399804004146 Protein of unknown function (DUF2982); Region: DUF2982; pfam11201 399804004147 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804004148 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 399804004149 Coenzyme A binding pocket [chemical binding]; other site 399804004150 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 399804004151 Transposase, Mutator family; Region: Transposase_mut; pfam00872 399804004152 MULE transposase domain; Region: MULE; pfam10551 399804004153 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 399804004154 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 399804004155 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 399804004156 UDP-glucose 4-epimerase; Region: PLN02240 399804004157 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 399804004158 NAD binding site [chemical binding]; other site 399804004159 homodimer interface [polypeptide binding]; other site 399804004160 active site 399804004161 substrate binding site [chemical binding]; other site 399804004162 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 399804004163 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 399804004164 active site 399804004165 tetramer interface; other site 399804004166 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 399804004167 cofactor binding site; other site 399804004168 metal binding site [ion binding]; metal-binding site 399804004169 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 399804004170 aromatic arch; other site 399804004171 DCoH dimer interaction site [polypeptide binding]; other site 399804004172 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 399804004173 DCoH tetramer interaction site [polypeptide binding]; other site 399804004174 substrate binding site [chemical binding]; other site 399804004175 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 399804004176 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 399804004177 putative aromatic amino acid binding site; other site 399804004178 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 399804004179 Walker A motif; other site 399804004180 ATP binding site [chemical binding]; other site 399804004181 Walker B motif; other site 399804004182 arginine finger; other site 399804004183 GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break...; Region: GIY-YIG_Cterm; cl11508 399804004184 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 399804004185 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 399804004186 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 399804004187 maleylacetoacetate isomerase; Region: maiA; TIGR01262 399804004188 C-terminal domain interface [polypeptide binding]; other site 399804004189 GSH binding site (G-site) [chemical binding]; other site 399804004190 putative dimer interface [polypeptide binding]; other site 399804004191 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 399804004192 dimer interface [polypeptide binding]; other site 399804004193 N-terminal domain interface [polypeptide binding]; other site 399804004194 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 399804004195 Bacterial protein of unknown function (DUF925); Region: DUF925; pfam06042 399804004196 outer membrane protein W; Provisional; Region: PRK10959 399804004197 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 399804004198 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804004199 NAD(P) binding site [chemical binding]; other site 399804004200 active site 399804004201 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 399804004202 homoserine O-succinyltransferase; Provisional; Region: PRK05368 399804004203 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 399804004204 proposed active site lysine [active] 399804004205 conserved cys residue [active] 399804004206 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 399804004207 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804004208 HAMP domain; Region: HAMP; pfam00672 399804004209 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804004210 dimer interface [polypeptide binding]; other site 399804004211 putative CheW interface [polypeptide binding]; other site 399804004212 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 399804004213 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 399804004214 dimer interface [polypeptide binding]; other site 399804004215 active site 399804004216 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 399804004217 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 399804004218 tetrameric interface [polypeptide binding]; other site 399804004219 NAD binding site [chemical binding]; other site 399804004220 catalytic residues [active] 399804004221 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 399804004222 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 399804004223 active site 399804004224 enoyl-CoA hydratase; Provisional; Region: PRK09076 399804004225 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 399804004226 substrate binding site [chemical binding]; other site 399804004227 oxyanion hole (OAH) forming residues; other site 399804004228 trimer interface [polypeptide binding]; other site 399804004229 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 399804004230 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 399804004231 substrate binding site [chemical binding]; other site 399804004232 oxyanion hole (OAH) forming residues; other site 399804004233 trimer interface [polypeptide binding]; other site 399804004234 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 399804004235 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 399804004236 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 399804004237 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 399804004238 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804004239 NAD(P) binding site [chemical binding]; other site 399804004240 active site 399804004241 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 399804004242 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804004243 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 399804004244 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 399804004245 DNA binding residues [nucleotide binding] 399804004246 dimer interface [polypeptide binding]; other site 399804004247 copper binding site [ion binding]; other site 399804004248 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 399804004249 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 399804004250 metal-binding site [ion binding] 399804004251 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 399804004252 Soluble P-type ATPase [General function prediction only]; Region: COG4087 399804004253 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 399804004254 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804004255 Walker A/P-loop; other site 399804004256 ATP binding site [chemical binding]; other site 399804004257 Q-loop/lid; other site 399804004258 ABC transporter signature motif; other site 399804004259 Walker B; other site 399804004260 D-loop; other site 399804004261 H-loop/switch region; other site 399804004262 ABC transporter; Region: ABC_tran_2; pfam12848 399804004263 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804004264 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 399804004265 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 399804004266 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 399804004267 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 399804004268 FAD binding domain; Region: FAD_binding_4; pfam01565 399804004269 Berberine and berberine like; Region: BBE; pfam08031 399804004270 PAS domain S-box; Region: sensory_box; TIGR00229 399804004271 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 399804004272 putative active site [active] 399804004273 heme pocket [chemical binding]; other site 399804004274 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804004275 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804004276 metal binding site [ion binding]; metal-binding site 399804004277 active site 399804004278 I-site; other site 399804004279 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804004280 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804004281 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804004282 Domain of unknown function (DUF1888); Region: DUF1888; pfam08985 399804004283 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 399804004284 DNA binding site [nucleotide binding] 399804004285 AAA ATPase domain; Region: AAA_16; pfam13191 399804004286 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804004287 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804004288 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804004289 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 399804004290 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804004291 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 399804004292 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 399804004293 Walker A/P-loop; other site 399804004294 ATP binding site [chemical binding]; other site 399804004295 Q-loop/lid; other site 399804004296 ABC transporter signature motif; other site 399804004297 Walker B; other site 399804004298 D-loop; other site 399804004299 H-loop/switch region; other site 399804004300 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 399804004301 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 399804004302 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 399804004303 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 399804004304 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 399804004305 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 399804004306 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 399804004307 Domain of unknown function (DUF4303); Region: DUF4303; pfam14136 399804004308 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 399804004309 dimerization interface [polypeptide binding]; other site 399804004310 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804004311 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804004312 dimer interface [polypeptide binding]; other site 399804004313 putative CheW interface [polypeptide binding]; other site 399804004314 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 399804004315 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 399804004316 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_24; cd09012 399804004317 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 399804004318 Histone chaperone Rttp106-like; Region: Rtt106; pfam08512 399804004319 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 399804004320 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 399804004321 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cd02116 399804004322 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 399804004323 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 399804004324 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 399804004325 conserved gate region; other site 399804004326 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 399804004327 ABC-ATPase subunit interface; other site 399804004328 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 399804004329 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 399804004330 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 399804004331 dimer interface [polypeptide binding]; other site 399804004332 conserved gate region; other site 399804004333 putative PBP binding loops; other site 399804004334 ABC-ATPase subunit interface; other site 399804004335 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 399804004336 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 399804004337 Walker A/P-loop; other site 399804004338 ATP binding site [chemical binding]; other site 399804004339 Q-loop/lid; other site 399804004340 ABC transporter signature motif; other site 399804004341 Walker B; other site 399804004342 D-loop; other site 399804004343 H-loop/switch region; other site 399804004344 transcriptional regulator PhoU; Provisional; Region: PRK11115 399804004345 PhoU domain; Region: PhoU; pfam01895 399804004346 PhoU domain; Region: PhoU; pfam01895 399804004347 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 399804004348 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804004349 HAMP domain; Region: HAMP; pfam00672 399804004350 dimerization interface [polypeptide binding]; other site 399804004351 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804004352 dimer interface [polypeptide binding]; other site 399804004353 putative CheW interface [polypeptide binding]; other site 399804004354 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 399804004355 dimer interface [polypeptide binding]; other site 399804004356 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 399804004357 metal binding site [ion binding]; metal-binding site 399804004358 Protein of unknown function (DUF502); Region: DUF502; pfam04367 399804004359 BCCT family transporter; Region: BCCT; pfam02028 399804004360 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 399804004361 active site 399804004362 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 399804004363 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 399804004364 S-adenosylmethionine binding site [chemical binding]; other site 399804004365 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09258 399804004366 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 399804004367 dimer interface [polypeptide binding]; other site 399804004368 active site 399804004369 CoA binding pocket [chemical binding]; other site 399804004370 haloalkane dehalogenase; Provisional; Region: PRK03592 399804004371 peptide synthase; Provisional; Region: PRK09274 399804004372 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 399804004373 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_1; cd05910 399804004374 acyl-activating enzyme (AAE) consensus motif; other site 399804004375 putative AMP binding site [chemical binding]; other site 399804004376 putative active site [active] 399804004377 putative CoA binding site [chemical binding]; other site 399804004378 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804004379 3-beta hydroxysteroid dehydrogenase/isomerase family; Region: 3Beta_HSD; pfam01073 399804004380 NAD(P) binding site [chemical binding]; other site 399804004381 active site 399804004382 Protein of unknown function (DUF3624); Region: DUF3624; pfam12292 399804004383 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 399804004384 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 399804004385 ABC-type multidrug transport system, ATPase component; Region: ABC_drug_resistance_like; cd03264 399804004386 Walker A/P-loop; other site 399804004387 ATP binding site [chemical binding]; other site 399804004388 Q-loop/lid; other site 399804004389 ABC transporter signature motif; other site 399804004390 Walker B; other site 399804004391 D-loop; other site 399804004392 H-loop/switch region; other site 399804004393 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 399804004394 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 399804004395 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 399804004396 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 399804004397 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 399804004398 Zn binding site [ion binding]; other site 399804004399 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 399804004400 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 399804004401 active site 399804004402 substrate binding site [chemical binding]; other site 399804004403 metal binding site [ion binding]; metal-binding site 399804004404 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 399804004405 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 399804004406 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 399804004407 Predicted transcriptional regulator [Transcription]; Region: COG2378 399804004408 HTH domain; Region: HTH_11; pfam08279 399804004409 WYL domain; Region: WYL; pfam13280 399804004410 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 399804004411 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 399804004412 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 399804004413 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804004414 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 399804004415 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804004416 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 399804004417 trimer interface [polypeptide binding]; other site 399804004418 active site 399804004419 substrate binding site [chemical binding]; other site 399804004420 CoA binding site [chemical binding]; other site 399804004421 Protein of unknown function (DUF1706); Region: DUF1706; pfam08020 399804004422 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 399804004423 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 399804004424 putative pyridoxal-dependent aspartate 1-decarboxylase; Region: NOD_PanD_pyr; TIGR03799 399804004425 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 399804004426 catalytic residue [active] 399804004427 Glycerate kinase [Carbohydrate transport and metabolism]; Region: COG1929 399804004428 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 399804004429 fructuronate transporter; Provisional; Region: PRK10034; cl15264 399804004430 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 399804004431 putative heme binding pocket [chemical binding]; other site 399804004432 carbohydrate diacid transcriptional activator CdaR; Provisional; Region: PRK11477 399804004433 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 399804004434 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 399804004435 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 399804004436 putative uracil binding site [chemical binding]; other site 399804004437 putative active site [active] 399804004438 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 399804004439 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 399804004440 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 399804004441 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 399804004442 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 399804004443 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 399804004444 heme-binding residues [chemical binding]; other site 399804004445 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 399804004446 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 399804004447 heme-binding residues [chemical binding]; other site 399804004448 FeoA domain; Region: FeoA; pfam04023 399804004449 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 399804004450 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 399804004451 G1 box; other site 399804004452 GTP/Mg2+ binding site [chemical binding]; other site 399804004453 Switch I region; other site 399804004454 G2 box; other site 399804004455 G3 box; other site 399804004456 Switch II region; other site 399804004457 G4 box; other site 399804004458 G5 box; other site 399804004459 Nucleoside recognition; Region: Gate; pfam07670 399804004460 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 399804004461 Nucleoside recognition; Region: Gate; pfam07670 399804004462 Nucleoside recognition; Region: Gate; pfam07670 399804004463 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 399804004464 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 399804004465 active site 399804004466 HIGH motif; other site 399804004467 nucleotide binding site [chemical binding]; other site 399804004468 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 399804004469 KMSKS motif; other site 399804004470 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 399804004471 Protein of unknown function (DUF1282); Region: DUF1282; pfam06930 399804004472 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 399804004473 active site 399804004474 dinuclear metal binding site [ion binding]; other site 399804004475 dimerization interface [polypeptide binding]; other site 399804004476 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 399804004477 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 399804004478 putative active site [active] 399804004479 putative metal binding site [ion binding]; other site 399804004480 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 399804004481 substrate binding site [chemical binding]; other site 399804004482 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 399804004483 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 399804004484 active site 399804004485 HIGH motif; other site 399804004486 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 399804004487 KMSKS motif; other site 399804004488 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 399804004489 tRNA binding surface [nucleotide binding]; other site 399804004490 anticodon binding site; other site 399804004491 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804004492 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804004493 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804004494 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804004495 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 399804004496 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 399804004497 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 399804004498 homodimer interface [polypeptide binding]; other site 399804004499 NADP binding site [chemical binding]; other site 399804004500 substrate binding site [chemical binding]; other site 399804004501 trigger factor; Provisional; Region: tig; PRK01490 399804004502 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804004503 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 399804004504 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 399804004505 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 399804004506 oligomer interface [polypeptide binding]; other site 399804004507 active site residues [active] 399804004508 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 399804004509 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 399804004510 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 399804004511 Walker A motif; other site 399804004512 ATP binding site [chemical binding]; other site 399804004513 Walker B motif; other site 399804004514 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 399804004515 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 399804004516 Found in ATP-dependent protease La (LON); Region: LON; smart00464 399804004517 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 399804004518 Walker A motif; other site 399804004519 ATP binding site [chemical binding]; other site 399804004520 Walker B motif; other site 399804004521 arginine finger; other site 399804004522 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 399804004523 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 399804004524 IHF dimer interface [polypeptide binding]; other site 399804004525 IHF - DNA interface [nucleotide binding]; other site 399804004526 periplasmic folding chaperone; Provisional; Region: PRK10788 399804004527 SurA N-terminal domain; Region: SurA_N_3; cl07813 399804004528 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 399804004529 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 399804004530 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 399804004531 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 399804004532 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 399804004533 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 399804004534 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 399804004535 Walker A/P-loop; other site 399804004536 ATP binding site [chemical binding]; other site 399804004537 Q-loop/lid; other site 399804004538 ABC transporter signature motif; other site 399804004539 Walker B; other site 399804004540 D-loop; other site 399804004541 H-loop/switch region; other site 399804004542 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 399804004543 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapD; COG4170 399804004544 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 399804004545 Walker A/P-loop; other site 399804004546 ATP binding site [chemical binding]; other site 399804004547 Q-loop/lid; other site 399804004548 ABC transporter signature motif; other site 399804004549 Walker B; other site 399804004550 D-loop; other site 399804004551 H-loop/switch region; other site 399804004552 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 399804004553 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 399804004554 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 399804004555 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 399804004556 dimer interface [polypeptide binding]; other site 399804004557 conserved gate region; other site 399804004558 putative PBP binding loops; other site 399804004559 ABC-ATPase subunit interface; other site 399804004560 antimicrobial peptide ABC transporter permease SapB; Provisional; Region: PRK15110 399804004561 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 399804004562 dimer interface [polypeptide binding]; other site 399804004563 conserved gate region; other site 399804004564 putative PBP binding loops; other site 399804004565 ABC-ATPase subunit interface; other site 399804004566 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 399804004567 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 399804004568 peptide binding site [polypeptide binding]; other site 399804004569 phage shock protein A; Region: phageshock_pspA; TIGR02977 399804004570 phage shock protein B; Provisional; Region: pspB; PRK09458 399804004571 phage shock protein C; Region: phageshock_pspC; TIGR02978 399804004572 PspC domain; Region: PspC; cl00864 399804004573 YcjX-like family, DUF463; Region: DUF463; pfam04317 399804004574 hypothetical protein; Provisional; Region: PRK05415 399804004575 Domain of unknown function (DUF697); Region: DUF697; pfam05128 399804004576 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 399804004577 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 399804004578 homodimer interface [polypeptide binding]; other site 399804004579 substrate-cofactor binding pocket; other site 399804004580 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804004581 catalytic residue [active] 399804004582 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 399804004583 Helix-hairpin-helix motif; Region: HHH; pfam00633 399804004584 Late competence development protein ComFB; Region: ComFB; pfam10719 399804004585 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 399804004586 Primosomal replication protein priB and priC; Region: priB_priC; cl11483 399804004587 hypothetical protein; Provisional; Region: PRK10621 399804004588 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 399804004589 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 399804004590 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 399804004591 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 399804004592 DNA polymerase II; Reviewed; Region: PRK05762 399804004593 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 399804004594 active site 399804004595 catalytic site [active] 399804004596 substrate binding site [chemical binding]; other site 399804004597 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 399804004598 active site 399804004599 metal-binding site 399804004600 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 399804004601 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 399804004602 trimer interface [polypeptide binding]; other site 399804004603 eyelet of channel; other site 399804004604 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804004605 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804004606 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804004607 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804004608 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 399804004609 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 399804004610 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 399804004611 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 399804004612 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 399804004613 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 399804004614 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 399804004615 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 399804004616 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 399804004617 TPR motif; other site 399804004618 binding surface 399804004619 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 399804004620 binding surface 399804004621 TPR motif; other site 399804004622 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 399804004623 TPR motif; other site 399804004624 binding surface 399804004625 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804004626 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804004627 metal binding site [ion binding]; metal-binding site 399804004628 active site 399804004629 I-site; other site 399804004630 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 399804004631 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 399804004632 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 399804004633 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 399804004634 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 399804004635 RNA binding surface [nucleotide binding]; other site 399804004636 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 399804004637 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 399804004638 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804004639 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 399804004640 dimerization interface [polypeptide binding]; other site 399804004641 substrate binding pocket [chemical binding]; other site 399804004642 hypothetical protein; Provisional; Region: PRK10621 399804004643 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 399804004644 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 399804004645 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 399804004646 active site 399804004647 metal binding site [ion binding]; metal-binding site 399804004648 DNA binding site [nucleotide binding] 399804004649 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 399804004650 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 399804004651 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 399804004652 Walker A/P-loop; other site 399804004653 ATP binding site [chemical binding]; other site 399804004654 Q-loop/lid; other site 399804004655 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 399804004656 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 399804004657 ABC transporter signature motif; other site 399804004658 Walker B; other site 399804004659 D-loop; other site 399804004660 H-loop/switch region; other site 399804004661 putative peptidase; Provisional; Region: PRK11649 399804004662 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 399804004663 Peptidase family M23; Region: Peptidase_M23; pfam01551 399804004664 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 399804004665 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 399804004666 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 399804004667 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 399804004668 ATP binding site [chemical binding]; other site 399804004669 Mg++ binding site [ion binding]; other site 399804004670 motif III; other site 399804004671 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 399804004672 nucleotide binding region [chemical binding]; other site 399804004673 ATP-binding site [chemical binding]; other site 399804004674 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 399804004675 active site 399804004676 nucleophile elbow; other site 399804004677 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 399804004678 ATP cone domain; Region: ATP-cone; pfam03477 399804004679 Class III ribonucleotide reductase; Region: RNR_III; cd01675 399804004680 effector binding site; other site 399804004681 active site 399804004682 Zn binding site [ion binding]; other site 399804004683 glycine loop; other site 399804004684 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; PRK11121 399804004685 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 399804004686 hypothetical protein; Provisional; Region: PRK11020 399804004687 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 399804004688 dimerization interface [polypeptide binding]; other site 399804004689 active site 399804004690 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 399804004691 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 399804004692 Carbon starvation protein CstA; Region: CstA; pfam02554 399804004693 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 399804004694 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 399804004695 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 399804004696 active site 399804004697 phosphorylation site [posttranslational modification] 399804004698 intermolecular recognition site; other site 399804004699 dimerization interface [polypeptide binding]; other site 399804004700 LytTr DNA-binding domain; Region: LytTR; smart00850 399804004701 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 399804004702 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 399804004703 GAF domain; Region: GAF; pfam01590 399804004704 Histidine kinase; Region: His_kinase; pfam06580 399804004705 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 399804004706 ATP binding site [chemical binding]; other site 399804004707 Mg2+ binding site [ion binding]; other site 399804004708 G-X-G motif; other site 399804004709 Protein of unknown function (DUF2492); Region: DUF2492; pfam10678 399804004710 ParA-like protein; Provisional; Region: PHA02518 399804004711 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 399804004712 P-loop; other site 399804004713 Magnesium ion binding site [ion binding]; other site 399804004714 PilZ domain; Region: PilZ; pfam07238 399804004715 Phosphate-starvation-inducible E; Region: PsiE; pfam06146 399804004716 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 399804004717 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 399804004718 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 399804004719 Competence protein; Region: Competence; pfam03772 399804004720 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 399804004721 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 399804004722 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 399804004723 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 399804004724 Walker A/P-loop; other site 399804004725 ATP binding site [chemical binding]; other site 399804004726 Q-loop/lid; other site 399804004727 ABC transporter signature motif; other site 399804004728 Walker B; other site 399804004729 D-loop; other site 399804004730 H-loop/switch region; other site 399804004731 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 399804004732 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 399804004733 Uncharacterized conserved protein [Function unknown]; Region: COG2835 399804004734 Predicted membrane protein [Function unknown]; Region: COG3235 399804004735 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 399804004736 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 399804004737 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 399804004738 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 399804004739 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 399804004740 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 399804004741 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 399804004742 Protein of unknown function (DUF445); Region: DUF445; pfam04286 399804004743 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 399804004744 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 399804004745 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 399804004746 cytidine deaminase; Provisional; Region: PRK09027 399804004747 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 399804004748 active site 399804004749 catalytic motif [active] 399804004750 Zn binding site [ion binding]; other site 399804004751 Cytidine and deoxycytidylate deaminase zinc-binding region; Region: dCMP_cyt_deam_2; pfam08211 399804004752 exonuclease I; Provisional; Region: sbcB; PRK11779 399804004753 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 399804004754 active site 399804004755 catalytic site [active] 399804004756 substrate binding site [chemical binding]; other site 399804004757 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 399804004758 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 399804004759 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 399804004760 S-adenosylmethionine binding site [chemical binding]; other site 399804004761 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 399804004762 DNA-binding site [nucleotide binding]; DNA binding site 399804004763 RNA-binding motif; other site 399804004764 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 399804004765 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 399804004766 homodimer interface [polypeptide binding]; other site 399804004767 oligonucleotide binding site [chemical binding]; other site 399804004768 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 399804004769 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 399804004770 RNA binding surface [nucleotide binding]; other site 399804004771 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 399804004772 active site 399804004773 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 399804004774 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 399804004775 motif II; other site 399804004776 Maf-like protein; Region: Maf; pfam02545 399804004777 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 399804004778 active site 399804004779 dimer interface [polypeptide binding]; other site 399804004780 hypothetical protein; Provisional; Region: PRK11193 399804004781 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 399804004782 putative phosphate acyltransferase; Provisional; Region: PRK05331 399804004783 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 399804004784 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 399804004785 dimer interface [polypeptide binding]; other site 399804004786 active site 399804004787 CoA binding pocket [chemical binding]; other site 399804004788 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 399804004789 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 399804004790 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 399804004791 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 399804004792 NAD(P) binding site [chemical binding]; other site 399804004793 homotetramer interface [polypeptide binding]; other site 399804004794 homodimer interface [polypeptide binding]; other site 399804004795 active site 399804004796 acyl carrier protein; Provisional; Region: acpP; PRK00982 399804004797 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 399804004798 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 399804004799 dimer interface [polypeptide binding]; other site 399804004800 active site 399804004801 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 399804004802 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 399804004803 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 399804004804 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 399804004805 active site 399804004806 phosphate binding residues; other site 399804004807 catalytic residues [active] 399804004808 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 399804004809 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 399804004810 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 399804004811 active site 399804004812 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 399804004813 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 399804004814 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 399804004815 N-terminal plug; other site 399804004816 ligand-binding site [chemical binding]; other site 399804004817 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 399804004818 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 399804004819 active site 399804004820 nucleophile elbow; other site 399804004821 asparagine synthetase B; Provisional; Region: asnB; PRK09431 399804004822 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 399804004823 active site 399804004824 dimer interface [polypeptide binding]; other site 399804004825 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 399804004826 Ligand Binding Site [chemical binding]; other site 399804004827 Molecular Tunnel; other site 399804004828 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 399804004829 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 399804004830 PA/protease or protease-like domain interface [polypeptide binding]; other site 399804004831 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 399804004832 Peptidase family M28; Region: Peptidase_M28; pfam04389 399804004833 metal binding site [ion binding]; metal-binding site 399804004834 UMP phosphatase; Provisional; Region: PRK10444 399804004835 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 399804004836 active site 399804004837 motif I; other site 399804004838 motif II; other site 399804004839 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 399804004840 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 399804004841 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 399804004842 active site 399804004843 substrate binding site [chemical binding]; other site 399804004844 cosubstrate binding site; other site 399804004845 catalytic site [active] 399804004846 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 399804004847 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 399804004848 dimerization interface [polypeptide binding]; other site 399804004849 putative ATP binding site [chemical binding]; other site 399804004850 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 399804004851 active site 399804004852 Predicted permease [General function prediction only]; Region: COG2056 399804004853 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 399804004854 peroxidase; Provisional; Region: PRK15000 399804004855 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 399804004856 dimer interface [polypeptide binding]; other site 399804004857 decamer (pentamer of dimers) interface [polypeptide binding]; other site 399804004858 catalytic triad [active] 399804004859 peroxidatic and resolving cysteines [active] 399804004860 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 399804004861 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 399804004862 dimer interface [polypeptide binding]; other site 399804004863 catalytic site [active] 399804004864 putative active site [active] 399804004865 putative substrate binding site [chemical binding]; other site 399804004866 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 399804004867 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804004868 ligand binding site [chemical binding]; other site 399804004869 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 399804004870 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804004871 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 399804004872 active site 399804004873 TolQ protein; Region: tolQ; TIGR02796 399804004874 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 399804004875 TolR protein; Region: tolR; TIGR02801 399804004876 TolA protein; Region: tolA_full; TIGR02794 399804004877 TolA C-terminal; Region: TolA; pfam06519 399804004878 translocation protein TolB; Provisional; Region: tolB; PRK04792 399804004879 TolB amino-terminal domain; Region: TolB_N; pfam04052 399804004880 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804004881 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804004882 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804004883 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804004884 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 399804004885 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804004886 ligand binding site [chemical binding]; other site 399804004887 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 399804004888 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 399804004889 binding surface 399804004890 TPR motif; other site 399804004891 hypothetical protein; Provisional; Region: PRK03641 399804004892 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; pfam09829 399804004893 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 399804004894 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 399804004895 active site 399804004896 metal binding site [ion binding]; metal-binding site 399804004897 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 399804004898 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 399804004899 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 399804004900 active site 399804004901 Zn binding site [ion binding]; other site 399804004902 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 399804004903 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 399804004904 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 399804004905 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804004906 Coenzyme A binding pocket [chemical binding]; other site 399804004907 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 399804004908 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 399804004909 substrate binding pocket [chemical binding]; other site 399804004910 membrane-bound complex binding site; other site 399804004911 hinge residues; other site 399804004912 Predicted membrane protein (DUF2157); Region: DUF2157; pfam09925 399804004913 Domain of unknown function (DUF4401); Region: DUF4401; pfam14351 399804004914 GDYXXLXY protein; Region: GDYXXLXY; pfam14345 399804004915 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 399804004916 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 399804004917 generic binding surface II; other site 399804004918 generic binding surface I; other site 399804004919 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 399804004920 putative active site [active] 399804004921 putative catalytic site [active] 399804004922 putative Mg binding site IVb [ion binding]; other site 399804004923 putative phosphate binding site [ion binding]; other site 399804004924 putative DNA binding site [nucleotide binding]; other site 399804004925 putative Mg binding site IVa [ion binding]; other site 399804004926 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 399804004927 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804004928 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 399804004929 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804004930 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804004931 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804004932 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 399804004933 HSP70 interaction site [polypeptide binding]; other site 399804004934 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 399804004935 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 399804004936 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 399804004937 S-adenosylmethionine binding site [chemical binding]; other site 399804004938 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 399804004939 S-adenosylmethionine binding site [chemical binding]; other site 399804004940 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 399804004941 ABC transporter ATPase component; Reviewed; Region: PRK11147 399804004942 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804004943 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804004944 ABC transporter; Region: ABC_tran_2; pfam12848 399804004945 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804004946 Protein of unknown function (DUF3466); Region: DUF3466; pfam11949 399804004947 ribosome modulation factor; Provisional; Region: PRK14563 399804004948 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 399804004949 active site 1 [active] 399804004950 dimer interface [polypeptide binding]; other site 399804004951 active site 2 [active] 399804004952 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 399804004953 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 399804004954 response regulator; Provisional; Region: PRK09483 399804004955 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 399804004956 active site 399804004957 phosphorylation site [posttranslational modification] 399804004958 intermolecular recognition site; other site 399804004959 dimerization interface [polypeptide binding]; other site 399804004960 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 399804004961 DNA binding residues [nucleotide binding] 399804004962 dimerization interface [polypeptide binding]; other site 399804004963 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 399804004964 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 399804004965 GIY-YIG motif/motif A; other site 399804004966 active site 399804004967 catalytic site [active] 399804004968 putative DNA binding site [nucleotide binding]; other site 399804004969 metal binding site [ion binding]; metal-binding site 399804004970 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 399804004971 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 399804004972 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 399804004973 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804004974 Walker A/P-loop; other site 399804004975 ATP binding site [chemical binding]; other site 399804004976 Q-loop/lid; other site 399804004977 ABC transporter signature motif; other site 399804004978 Walker B; other site 399804004979 D-loop; other site 399804004980 H-loop/switch region; other site 399804004981 hypothetical protein; Provisional; Region: PRK11239 399804004982 Protein of unknown function, DUF480; Region: DUF480; pfam04337 399804004983 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 399804004984 S1 domain; Region: S1_2; pfam13509 399804004985 arginine decarboxylase; Provisional; Region: PRK05354 399804004986 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 399804004987 dimer interface [polypeptide binding]; other site 399804004988 active site 399804004989 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 399804004990 catalytic residues [active] 399804004991 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 399804004992 Adenosylmethionine decarboxylase; Region: SAM_decarbox; cl03253 399804004993 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 399804004994 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 399804004995 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 399804004996 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 399804004997 YceI-like domain; Region: YceI; pfam04264 399804004998 Protein of unknown function (DUF3802); Region: DUF3802; pfam12290 399804004999 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 399804005000 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 399804005001 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 399804005002 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 399804005003 nucleotide binding site/active site [active] 399804005004 HIT family signature motif; other site 399804005005 catalytic residue [active] 399804005006 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 399804005007 CoenzymeA binding site [chemical binding]; other site 399804005008 subunit interaction site [polypeptide binding]; other site 399804005009 PHB binding site; other site 399804005010 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 399804005011 CoenzymeA binding site [chemical binding]; other site 399804005012 subunit interaction site [polypeptide binding]; other site 399804005013 PHB binding site; other site 399804005014 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG5633 399804005015 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 399804005016 putative dimer interface [polypeptide binding]; other site 399804005017 purine nucleoside phosphorylase; Provisional; Region: PRK13374 399804005018 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 399804005019 putative transporter; Provisional; Region: PRK03699 399804005020 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 399804005021 putative substrate translocation pore; other site 399804005022 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 399804005023 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 399804005024 ligand binding site [chemical binding]; other site 399804005025 flexible hinge region; other site 399804005026 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 399804005027 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 399804005028 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 399804005029 N-terminal plug; other site 399804005030 ligand-binding site [chemical binding]; other site 399804005031 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 399804005032 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 399804005033 Phosphotransferase enzyme family; Region: APH; pfam01636 399804005034 active site 399804005035 ATP binding site [chemical binding]; other site 399804005036 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 399804005037 substrate binding site [chemical binding]; other site 399804005038 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 399804005039 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 399804005040 putative FMN binding site [chemical binding]; other site 399804005041 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 399804005042 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 399804005043 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 399804005044 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 399804005045 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 399804005046 Protein of unknown function, DUF482; Region: DUF482; pfam04339 399804005047 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 399804005048 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 399804005049 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 399804005050 dimer interface [polypeptide binding]; other site 399804005051 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 399804005052 active site 399804005053 Fe binding site [ion binding]; other site 399804005054 homogentisate 1,2-dioxygenase; Region: HgmA; cl17306 399804005055 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804005056 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804005057 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 399804005058 dimerization interface [polypeptide binding]; other site 399804005059 Mitochondrial biogenesis AIM24; Region: AIM24; pfam01987 399804005060 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 399804005061 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 399804005062 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804005063 Polysaccharide biosynthesis protein; Region: Polysacc_synt_3; pfam13440 399804005064 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 399804005065 Uncharacterized conserved protein [Function unknown]; Region: COG2947 399804005066 AMP-binding domain protein; Validated; Region: PRK08315 399804005067 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 399804005068 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 399804005069 acyl-activating enzyme (AAE) consensus motif; other site 399804005070 putative AMP binding site [chemical binding]; other site 399804005071 putative active site [active] 399804005072 putative CoA binding site [chemical binding]; other site 399804005073 Cache domain; Region: Cache_1; pfam02743 399804005074 PAS fold; Region: PAS_4; pfam08448 399804005075 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 399804005076 putative active site [active] 399804005077 heme pocket [chemical binding]; other site 399804005078 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804005079 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 399804005080 Mg2+ binding site [ion binding]; other site 399804005081 G-X-G motif; other site 399804005082 disulfide bond formation protein B; Provisional; Region: PRK01749 399804005083 sodium/proton antiporter; Reviewed; Region: nhaB; PRK09547 399804005084 fatty acid metabolism regulator; Provisional; Region: PRK04984 399804005085 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804005086 DNA-binding site [nucleotide binding]; DNA binding site 399804005087 FadR C-terminal domain; Region: FadR_C; pfam07840 399804005088 SpoVR family protein; Provisional; Region: PRK11767 399804005089 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 399804005090 hypothetical protein; Provisional; Region: PRK05325 399804005091 PrkA family serine protein kinase; Provisional; Region: PRK15455 399804005092 AAA ATPase domain; Region: AAA_16; pfam13191 399804005093 Walker A motif; other site 399804005094 ATP binding site [chemical binding]; other site 399804005095 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 399804005096 superoxide dismutase; Provisional; Region: PRK10543 399804005097 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 399804005098 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 399804005099 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 399804005100 putative GSH binding site [chemical binding]; other site 399804005101 catalytic residues [active] 399804005102 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 399804005103 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 399804005104 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 399804005105 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 399804005106 Walker A motif; other site 399804005107 ATP binding site [chemical binding]; other site 399804005108 Walker B motif; other site 399804005109 arginine finger; other site 399804005110 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 399804005111 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 399804005112 ArsC family; Region: ArsC; pfam03960 399804005113 catalytic residues [active] 399804005114 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 399804005115 Peptidase family M48; Region: Peptidase_M48; cl12018 399804005116 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 399804005117 binding surface 399804005118 TPR motif; other site 399804005119 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 399804005120 CPxP motif; other site 399804005121 Domain of unknown function DUF20; Region: UPF0118; pfam01594 399804005122 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 399804005123 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 399804005124 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804005125 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 399804005126 putative dimerization interface [polypeptide binding]; other site 399804005127 Lysine efflux permease [General function prediction only]; Region: COG1279 399804005128 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 399804005129 catalytic triad [active] 399804005130 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 399804005131 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_1; cd04893 399804005132 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 399804005133 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 399804005134 dihydrodipicolinate synthase; Region: dapA; TIGR00674 399804005135 dimer interface [polypeptide binding]; other site 399804005136 active site 399804005137 catalytic residue [active] 399804005138 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 399804005139 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 399804005140 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804005141 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804005142 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804005143 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804005144 Protein export membrane protein; Region: SecD_SecF; cl14618 399804005145 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 399804005146 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804005147 Coenzyme A binding pocket [chemical binding]; other site 399804005148 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 399804005149 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 399804005150 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 399804005151 hypothetical protein; Provisional; Region: PRK10621 399804005152 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 399804005153 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 399804005154 CRISPR/Cas system-associated RAMP superfamily protein Cmr1; Region: Cmr1_III-B; cl17436 399804005155 CRISPR/Cas system-associated protein Cas10; Region: Cas10_III; cl13853 399804005156 CRISPR-associated protein Cas10/Cmr2, subtype III-B; Region: cas_TM1794_Cmr2; TIGR02577 399804005157 CRISPR-associated protein (Cas_Cmr3); Region: Cas_Cmr3; pfam09700 399804005158 CRISPR/Cas system-associated RAMP superfamily protein Cmr3; Region: Cmr3_III-B; cd09748 399804005159 CRISPR/Cas system-associated RAMP superfamily protein Cmr4; Region: Cmr4_III-B; cl17440 399804005160 CRISPR/Cas system-associated protein Cmr5; Region: Cmr5_III-B; cd09749 399804005161 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl17214 399804005162 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 399804005163 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 399804005164 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 399804005165 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 399804005166 active site 399804005167 catalytic residues [active] 399804005168 metal binding site [ion binding]; metal-binding site 399804005169 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 399804005170 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 399804005171 ATP-grasp domain; Region: ATP-grasp_4; cl17255 399804005172 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 399804005173 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 399804005174 carboxyltransferase (CT) interaction site; other site 399804005175 biotinylation site [posttranslational modification]; other site 399804005176 enoyl-CoA hydratase; Provisional; Region: PRK05995 399804005177 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 399804005178 substrate binding site [chemical binding]; other site 399804005179 oxyanion hole (OAH) forming residues; other site 399804005180 trimer interface [polypeptide binding]; other site 399804005181 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 399804005182 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 399804005183 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 399804005184 isovaleryl-CoA dehydrogenase; Region: PLN02519 399804005185 substrate binding site [chemical binding]; other site 399804005186 FAD binding site [chemical binding]; other site 399804005187 catalytic base [active] 399804005188 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 399804005189 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 399804005190 DNA binding residues [nucleotide binding] 399804005191 putative dimer interface [polypeptide binding]; other site 399804005192 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 399804005193 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 399804005194 acyl-activating enzyme (AAE) consensus motif; other site 399804005195 AMP binding site [chemical binding]; other site 399804005196 active site 399804005197 CoA binding site [chemical binding]; other site 399804005198 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 399804005199 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 399804005200 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 399804005201 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 399804005202 Peptidase S8 family domain in Protein convertases; Region: Peptidases_S8_Protein_convertases_Kexins_Furin-lik; cd04059 399804005203 calcium binding site 1 [ion binding]; other site 399804005204 active site 399804005205 catalytic triad [active] 399804005206 calcium binding site 2 [ion binding]; other site 399804005207 calcium binding site 3 [ion binding]; other site 399804005208 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 399804005209 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804005210 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804005211 LysR substrate binding domain; Region: LysR_substrate; pfam03466 399804005212 dimerization interface [polypeptide binding]; other site 399804005213 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 399804005214 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 399804005215 putative active site [active] 399804005216 metal binding site [ion binding]; metal-binding site 399804005217 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 399804005218 UbiA prenyltransferase family; Region: UbiA; pfam01040 399804005219 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 399804005220 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804005221 NAD(P) binding site [chemical binding]; other site 399804005222 active site 399804005223 acyl-CoA thioesterase II; Provisional; Region: PRK10526 399804005224 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 399804005225 active site 399804005226 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 399804005227 catalytic triad [active] 399804005228 dimer interface [polypeptide binding]; other site 399804005229 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 399804005230 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804005231 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804005232 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 399804005233 dimerization interface [polypeptide binding]; other site 399804005234 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 399804005235 Major Facilitator Superfamily; Region: MFS_1; pfam07690 399804005236 putative substrate translocation pore; other site 399804005237 exopolyphosphatase; Region: exo_poly_only; TIGR03706 399804005238 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 399804005239 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 399804005240 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 399804005241 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 399804005242 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 399804005243 domain interface [polypeptide binding]; other site 399804005244 active site 399804005245 catalytic site [active] 399804005246 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 399804005247 domain interface [polypeptide binding]; other site 399804005248 active site 399804005249 catalytic site [active] 399804005250 putative chaperone; Provisional; Region: PRK11678 399804005251 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 399804005252 nucleotide binding site [chemical binding]; other site 399804005253 putative NEF/HSP70 interaction site [polypeptide binding]; other site 399804005254 SBD interface [polypeptide binding]; other site 399804005255 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 399804005256 CreA protein; Region: CreA; pfam05981 399804005257 cystathionine beta-lyase; Provisional; Region: PRK09028 399804005258 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 399804005259 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 399804005260 catalytic residue [active] 399804005261 proteobacterial dedicated sortase system histidine kinase; Region: marine_sort_HK; TIGR03785 399804005262 DOMON-like type 9 carbohydrate binding module at the N-terminus of bacterial sensor histidine kinases; Region: CBM9_like_HisKa; cd09622 399804005263 putative ligand binding site [chemical binding]; other site 399804005264 HAMP domain; Region: HAMP; pfam00672 399804005265 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 399804005266 dimer interface [polypeptide binding]; other site 399804005267 phosphorylation site [posttranslational modification] 399804005268 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 399804005269 ATP binding site [chemical binding]; other site 399804005270 Mg2+ binding site [ion binding]; other site 399804005271 G-X-G motif; other site 399804005272 proteobacterial dedicated sortase system response regulator; Region: marine_sort_RR; TIGR03787 399804005273 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 399804005274 active site 399804005275 phosphorylation site [posttranslational modification] 399804005276 intermolecular recognition site; other site 399804005277 dimerization interface [polypeptide binding]; other site 399804005278 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 399804005279 DNA binding site [nucleotide binding] 399804005280 Vault protein inter-alpha-trypsin domain; Region: VIT; cl02699 399804005281 marine proteobacterial sortase target protein; Region: marine_srt_targ; TIGR03788 399804005282 vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to...; Region: vWA_interalpha_trypsin_inhibitor; cd01461 399804005283 metal ion-dependent adhesion site (MIDAS); other site 399804005284 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved...; Region: Sortase_D_4; cd05828 399804005285 active site 399804005286 catalytic site [active] 399804005287 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804005288 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804005289 metal binding site [ion binding]; metal-binding site 399804005290 active site 399804005291 I-site; other site 399804005292 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 399804005293 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 399804005294 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 399804005295 PA/protease or protease-like domain interface [polypeptide binding]; other site 399804005296 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 399804005297 metal binding site [ion binding]; metal-binding site 399804005298 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 399804005299 ATP-grasp domain; Region: ATP-grasp_4; cl17255 399804005300 hypothetical protein; Provisional; Region: PRK11027 399804005301 transcriptional regulator HdfR; Provisional; Region: PRK03601 399804005302 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804005303 LysR substrate binding domain; Region: LysR_substrate; pfam03466 399804005304 dimerization interface [polypeptide binding]; other site 399804005305 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 399804005306 DNA ligase; Provisional; Region: PRK09125 399804005307 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 399804005308 DNA binding site [nucleotide binding] 399804005309 active site 399804005310 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 399804005311 DNA binding site [nucleotide binding] 399804005312 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 399804005313 Low molecular weight phosphatase family; Region: LMWPc; cd00115 399804005314 active site 399804005315 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804005316 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804005317 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804005318 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804005319 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 399804005320 E3 interaction surface; other site 399804005321 lipoyl attachment site [posttranslational modification]; other site 399804005322 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804005323 MltA-interacting protein MipA; Region: MipA; cl01504 399804005324 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 399804005325 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 399804005326 GTP/Mg2+ binding site [chemical binding]; other site 399804005327 G4 box; other site 399804005328 G5 box; other site 399804005329 G1 box; other site 399804005330 Switch I region; other site 399804005331 G2 box; other site 399804005332 G3 box; other site 399804005333 Switch II region; other site 399804005334 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 399804005335 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 399804005336 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 399804005337 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 399804005338 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 399804005339 methionine sulfoxide reductase A; Provisional; Region: PRK14054 399804005340 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; cd00384 399804005341 dimer interface [polypeptide binding]; other site 399804005342 active site 399804005343 Schiff base residues; other site 399804005344 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 399804005345 Glycoprotease family; Region: Peptidase_M22; pfam00814 399804005346 Peptidase M50B-like; Region: Peptidase_M50B; pfam13398 399804005347 Predicted methyltransferase [General function prediction only]; Region: COG4798 399804005348 Methyltransferase domain; Region: Methyltransf_23; pfam13489 399804005349 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 399804005350 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 399804005351 PGAP1-like protein; Region: PGAP1; pfam07819 399804005352 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 399804005353 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 399804005354 acyl-activating enzyme (AAE) consensus motif; other site 399804005355 putative AMP binding site [chemical binding]; other site 399804005356 putative active site [active] 399804005357 putative CoA binding site [chemical binding]; other site 399804005358 ribonuclease D; Region: rnd; TIGR01388 399804005359 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 399804005360 catalytic site [active] 399804005361 putative active site [active] 399804005362 putative substrate binding site [chemical binding]; other site 399804005363 HRDC domain; Region: HRDC; pfam00570 399804005364 cell division topological specificity factor MinE; Reviewed; Region: minE; PRK00296 399804005365 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 399804005366 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 399804005367 Switch I; other site 399804005368 Switch II; other site 399804005369 septum formation inhibitor; Reviewed; Region: minC; PRK04804 399804005370 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 399804005371 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 399804005372 YcgL domain; Region: YcgL; pfam05166 399804005373 hypothetical protein; Provisional; Region: PRK05170 399804005374 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 399804005375 substrate binding site [chemical binding]; other site 399804005376 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 399804005377 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 399804005378 ATP binding site [chemical binding]; other site 399804005379 Mg++ binding site [ion binding]; other site 399804005380 motif III; other site 399804005381 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 399804005382 nucleotide binding region [chemical binding]; other site 399804005383 ATP-binding site [chemical binding]; other site 399804005384 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 399804005385 ribonuclease activity regulator protein RraA; Reviewed; Region: PRK12487 399804005386 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 399804005387 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 399804005388 Intracellular proteinase inhibitor; Region: BsuPI; pfam12690 399804005389 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 399804005390 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 399804005391 N-acetyl-D-glucosamine binding site [chemical binding]; other site 399804005392 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804005393 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804005394 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804005395 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 399804005396 Methyltransferase domain; Region: Methyltransf_11; pfam08241 399804005397 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 399804005398 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804005399 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 399804005400 putative dimerization interface [polypeptide binding]; other site 399804005401 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 399804005402 RNA/DNA hybrid binding site [nucleotide binding]; other site 399804005403 active site 399804005404 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 399804005405 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 399804005406 active site 399804005407 catalytic site [active] 399804005408 substrate binding site [chemical binding]; other site 399804005409 TIGR03503 family protein; Region: TIGR03503 399804005410 alpha-galactosidase; Provisional; Region: PRK15076 399804005411 Protein of unknown function (DUF1318); Region: DUF1318; pfam07027 399804005412 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 399804005413 Dicarboxylate transport; Region: DctA-YdbH; pfam11739 399804005414 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 399804005415 aromatic amino acid transport protein; Region: araaP; TIGR00837 399804005416 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 399804005417 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 399804005418 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 399804005419 metal binding site [ion binding]; metal-binding site 399804005420 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 399804005421 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 399804005422 substrate binding site [chemical binding]; other site 399804005423 glutamase interaction surface [polypeptide binding]; other site 399804005424 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 399804005425 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 399804005426 catalytic residues [active] 399804005427 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 399804005428 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 399804005429 putative active site [active] 399804005430 oxyanion strand; other site 399804005431 catalytic triad [active] 399804005432 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 399804005433 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 399804005434 active site 399804005435 motif I; other site 399804005436 motif II; other site 399804005437 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 399804005438 putative active site pocket [active] 399804005439 4-fold oligomerization interface [polypeptide binding]; other site 399804005440 metal binding residues [ion binding]; metal-binding site 399804005441 3-fold/trimer interface [polypeptide binding]; other site 399804005442 histidinol-phosphate aminotransferase; Provisional; Region: PRK04635 399804005443 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 399804005444 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804005445 homodimer interface [polypeptide binding]; other site 399804005446 catalytic residue [active] 399804005447 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 399804005448 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 399804005449 NAD binding site [chemical binding]; other site 399804005450 dimerization interface [polypeptide binding]; other site 399804005451 product binding site; other site 399804005452 substrate binding site [chemical binding]; other site 399804005453 zinc binding site [ion binding]; other site 399804005454 catalytic residues [active] 399804005455 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 399804005456 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 399804005457 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 399804005458 Protein of unknown function (DUF938); Region: DUF938; pfam06080 399804005459 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 399804005460 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 399804005461 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804005462 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804005463 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 399804005464 putative effector binding pocket; other site 399804005465 putative dimerization interface [polypeptide binding]; other site 399804005466 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 399804005467 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 399804005468 substrate binding site [chemical binding]; other site 399804005469 catalytic Zn binding site [ion binding]; other site 399804005470 NAD binding site [chemical binding]; other site 399804005471 structural Zn binding site [ion binding]; other site 399804005472 dimer interface [polypeptide binding]; other site 399804005473 S-formylglutathione hydrolase; Region: PLN02442 399804005474 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 399804005475 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 399804005476 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 399804005477 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 399804005478 beta-hexosaminidase; Provisional; Region: PRK05337 399804005479 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 399804005480 hypothetical protein; Provisional; Region: PRK04940 399804005481 SEC-C motif; Region: SEC-C; pfam02810 399804005482 Domain of unknown function (DUF4263); Region: DUF4263; pfam14082 399804005483 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804005484 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804005485 acylphosphatase; Provisional; Region: PRK14429 399804005486 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 399804005487 transcription-repair coupling factor; Provisional; Region: PRK10689 399804005488 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 399804005489 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 399804005490 ATP binding site [chemical binding]; other site 399804005491 putative Mg++ binding site [ion binding]; other site 399804005492 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 399804005493 nucleotide binding region [chemical binding]; other site 399804005494 ATP-binding site [chemical binding]; other site 399804005495 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 399804005496 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 399804005497 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 399804005498 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 399804005499 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 399804005500 Walker A/P-loop; other site 399804005501 ATP binding site [chemical binding]; other site 399804005502 Q-loop/lid; other site 399804005503 ABC transporter signature motif; other site 399804005504 Walker B; other site 399804005505 D-loop; other site 399804005506 H-loop/switch region; other site 399804005507 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 399804005508 FtsX-like permease family; Region: FtsX; pfam02687 399804005509 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 399804005510 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 399804005511 active site 399804005512 dimerization interface [polypeptide binding]; other site 399804005513 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 399804005514 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 399804005515 serine O-acetyltransferase; Region: cysE; TIGR01172 399804005516 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 399804005517 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 399804005518 trimer interface [polypeptide binding]; other site 399804005519 active site 399804005520 substrate binding site [chemical binding]; other site 399804005521 CoA binding site [chemical binding]; other site 399804005522 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 399804005523 Rrf2 family protein; Region: rrf2_super; TIGR00738 399804005524 cysteine desulfurase; Provisional; Region: PRK14012 399804005525 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 399804005526 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 399804005527 catalytic residue [active] 399804005528 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 399804005529 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 399804005530 trimerization site [polypeptide binding]; other site 399804005531 active site 399804005532 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 399804005533 co-chaperone HscB; Provisional; Region: hscB; PRK05014 399804005534 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 399804005535 HSP70 interaction site [polypeptide binding]; other site 399804005536 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 399804005537 chaperone protein HscA; Provisional; Region: hscA; PRK05183 399804005538 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 399804005539 nucleotide binding site [chemical binding]; other site 399804005540 putative NEF/HSP70 interaction site [polypeptide binding]; other site 399804005541 SBD interface [polypeptide binding]; other site 399804005542 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 399804005543 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 399804005544 catalytic loop [active] 399804005545 iron binding site [ion binding]; other site 399804005546 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 399804005547 ATP-grasp domain; Region: ATP-grasp_4; cl17255 399804005548 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 399804005549 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 399804005550 active site 399804005551 multimer interface [polypeptide binding]; other site 399804005552 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 399804005553 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 399804005554 putative dimer interface [polypeptide binding]; other site 399804005555 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 399804005556 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 399804005557 putative valine binding site [chemical binding]; other site 399804005558 dimer interface [polypeptide binding]; other site 399804005559 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 399804005560 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK08979 399804005561 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 399804005562 PYR/PP interface [polypeptide binding]; other site 399804005563 dimer interface [polypeptide binding]; other site 399804005564 TPP binding site [chemical binding]; other site 399804005565 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 399804005566 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 399804005567 TPP-binding site [chemical binding]; other site 399804005568 dimer interface [polypeptide binding]; other site 399804005569 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 399804005570 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 399804005571 putative substrate translocation pore; other site 399804005572 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 399804005573 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 399804005574 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804005575 DNA-binding site [nucleotide binding]; DNA binding site 399804005576 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 399804005577 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804005578 homodimer interface [polypeptide binding]; other site 399804005579 catalytic residue [active] 399804005580 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 399804005581 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 399804005582 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 399804005583 Sulfate transporter family; Region: Sulfate_transp; pfam00916 399804005584 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 399804005585 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 399804005586 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 399804005587 active site residue [active] 399804005588 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804005589 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804005590 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804005591 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804005592 Protein of unknown function (DUF2897); Region: DUF2897; pfam11446 399804005593 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 399804005594 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 399804005595 Ligand binding site; other site 399804005596 oligomer interface; other site 399804005597 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 399804005598 active site clefts [active] 399804005599 zinc binding site [ion binding]; other site 399804005600 dimer interface [polypeptide binding]; other site 399804005601 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 399804005602 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 399804005603 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 399804005604 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 399804005605 metal binding site [ion binding]; metal-binding site 399804005606 dimer interface [polypeptide binding]; other site 399804005607 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 399804005608 ArsC family; Region: ArsC; pfam03960 399804005609 putative catalytic residues [active] 399804005610 Vibrio chemotaxis protein N terminus; Region: MCP_N; pfam05581 399804005611 Cache domain; Region: Cache_1; pfam02743 399804005612 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 399804005613 dimerization interface [polypeptide binding]; other site 399804005614 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804005615 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804005616 dimer interface [polypeptide binding]; other site 399804005617 putative CheW interface [polypeptide binding]; other site 399804005618 PTS system glucose-specific transporter subunit; Provisional; Region: PRK09439 399804005619 HPr interaction site; other site 399804005620 glycerol kinase (GK) interaction site [polypeptide binding]; other site 399804005621 active site 399804005622 phosphorylation site [posttranslational modification] 399804005623 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 399804005624 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 399804005625 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 399804005626 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 399804005627 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 399804005628 dimerization domain swap beta strand [polypeptide binding]; other site 399804005629 regulatory protein interface [polypeptide binding]; other site 399804005630 active site 399804005631 regulatory phosphorylation site [posttranslational modification]; other site 399804005632 Uncharacterized conserved protein [Function unknown]; Region: COG3603 399804005633 Family description; Region: ACT_7; pfam13840 399804005634 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 399804005635 Cache domain; Region: Cache_2; cl07034 399804005636 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 399804005637 dimerization interface [polypeptide binding]; other site 399804005638 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804005639 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804005640 dimer interface [polypeptide binding]; other site 399804005641 putative CheW interface [polypeptide binding]; other site 399804005642 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 399804005643 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 399804005644 active site 399804005645 catalytic site [active] 399804005646 substrate binding site [chemical binding]; other site 399804005647 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 399804005648 AAA domain; Region: AAA_30; pfam13604 399804005649 Family description; Region: UvrD_C_2; pfam13538 399804005650 exodeoxyribonuclease V, beta subunit; Region: recB; TIGR00609 399804005651 Part of AAA domain; Region: AAA_19; pfam13245 399804005652 Family description; Region: UvrD_C_2; pfam13538 399804005653 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 399804005654 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 399804005655 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 399804005656 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 399804005657 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 399804005658 Protein of unknown function DUF58; Region: DUF58; pfam01882 399804005659 MoxR-like ATPases [General function prediction only]; Region: COG0714 399804005660 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 399804005661 Walker A motif; other site 399804005662 ATP binding site [chemical binding]; other site 399804005663 Walker B motif; other site 399804005664 arginine finger; other site 399804005665 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 399804005666 lytic murein transglycosylase; Provisional; Region: PRK11619 399804005667 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 399804005668 N-acetyl-D-glucosamine binding site [chemical binding]; other site 399804005669 catalytic residue [active] 399804005670 DNA recombination protein RmuC; Provisional; Region: PRK10361 399804005671 RmuC family; Region: RmuC; pfam02646 399804005672 TMAO/DMSO reductase; Reviewed; Region: PRK05363 399804005673 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 399804005674 Moco binding site; other site 399804005675 metal coordination site [ion binding]; other site 399804005676 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 399804005677 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 399804005678 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 399804005679 dimer interface [polypeptide binding]; other site 399804005680 active site 399804005681 metal binding site [ion binding]; metal-binding site 399804005682 glutathione binding site [chemical binding]; other site 399804005683 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 399804005684 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 399804005685 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 399804005686 MarR family; Region: MarR; pfam01047 399804005687 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 399804005688 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804005689 putative metal dependent hydrolase; Provisional; Region: PRK11598 399804005690 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 399804005691 Sulfatase; Region: Sulfatase; pfam00884 399804005692 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804005693 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804005694 metal binding site [ion binding]; metal-binding site 399804005695 active site 399804005696 I-site; other site 399804005697 universal stress protein UspE; Provisional; Region: PRK11175 399804005698 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 399804005699 Ligand Binding Site [chemical binding]; other site 399804005700 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 399804005701 Ligand Binding Site [chemical binding]; other site 399804005702 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 399804005703 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 399804005704 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 399804005705 TrkA-N domain; Region: TrkA_N; pfam02254 399804005706 Acylphosphatase; Region: Acylphosphatase; pfam00708 399804005707 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 399804005708 HypF finger; Region: zf-HYPF; pfam07503 399804005709 HypF finger; Region: zf-HYPF; pfam07503 399804005710 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 399804005711 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 399804005712 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 399804005713 putative substrate-binding site; other site 399804005714 nickel binding site [ion binding]; other site 399804005715 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 399804005716 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 399804005717 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 399804005718 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 399804005719 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 399804005720 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 399804005721 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 399804005722 catalytic residues [active] 399804005723 Domain of unknown function (DUF4266); Region: DUF4266; pfam14086 399804005724 Protein of unknown function (DUF3570); Region: DUF3570; pfam12094 399804005725 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 399804005726 ApbE family; Region: ApbE; pfam02424 399804005727 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804005728 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 399804005729 active site 399804005730 phosphorylation site [posttranslational modification] 399804005731 intermolecular recognition site; other site 399804005732 dimerization interface [polypeptide binding]; other site 399804005733 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 399804005734 DNA binding site [nucleotide binding] 399804005735 sensor protein QseC; Provisional; Region: PRK10337 399804005736 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 399804005737 dimer interface [polypeptide binding]; other site 399804005738 phosphorylation site [posttranslational modification] 399804005739 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 399804005740 ATP binding site [chemical binding]; other site 399804005741 Mg2+ binding site [ion binding]; other site 399804005742 G-X-G motif; other site 399804005743 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 399804005744 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 399804005745 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 399804005746 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 399804005747 Ligand binding site; other site 399804005748 DXD motif; other site 399804005749 glutamyl-tRNA(Gln) amidotransferase, subunit D; Region: gatD_arch; TIGR02153 399804005750 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 399804005751 active site 399804005752 homodimer interface [polypeptide binding]; other site 399804005753 protease 4; Provisional; Region: PRK10949 399804005754 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 399804005755 tandem repeat interface [polypeptide binding]; other site 399804005756 oligomer interface [polypeptide binding]; other site 399804005757 active site residues [active] 399804005758 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 399804005759 tandem repeat interface [polypeptide binding]; other site 399804005760 oligomer interface [polypeptide binding]; other site 399804005761 active site residues [active] 399804005762 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 399804005763 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 399804005764 active site 399804005765 FMN binding site [chemical binding]; other site 399804005766 2,4-decadienoyl-CoA binding site; other site 399804005767 catalytic residue [active] 399804005768 4Fe-4S cluster binding site [ion binding]; other site 399804005769 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 399804005770 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 399804005771 YCII-related domain; Region: YCII; pfam03795 399804005772 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 399804005773 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 399804005774 catalytic loop [active] 399804005775 iron binding site [ion binding]; other site 399804005776 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 399804005777 dimer interface [polypeptide binding]; other site 399804005778 putative radical transfer pathway; other site 399804005779 diiron center [ion binding]; other site 399804005780 tyrosyl radical; other site 399804005781 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 399804005782 ATP cone domain; Region: ATP-cone; pfam03477 399804005783 Class I ribonucleotide reductase; Region: RNR_I; cd01679 399804005784 active site 399804005785 dimer interface [polypeptide binding]; other site 399804005786 catalytic residues [active] 399804005787 effector binding site; other site 399804005788 R2 peptide binding site; other site 399804005789 phosphoglycolate phosphatase; Provisional; Region: PRK13222 399804005790 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 399804005791 active site 399804005792 motif I; other site 399804005793 motif II; other site 399804005794 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 399804005795 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 399804005796 S-adenosylmethionine binding site [chemical binding]; other site 399804005797 DNA gyrase subunit A; Validated; Region: PRK05560 399804005798 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 399804005799 CAP-like domain; other site 399804005800 active site 399804005801 primary dimer interface [polypeptide binding]; other site 399804005802 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 399804005803 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 399804005804 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 399804005805 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 399804005806 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 399804005807 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 399804005808 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 399804005809 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 399804005810 catalytic residue [active] 399804005811 ribulokinase; Provisional; Region: PRK04123 399804005812 Ribulokinases; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_RBK; cd07781 399804005813 N- and C-terminal domain interface [polypeptide binding]; other site 399804005814 active site 399804005815 MgATP binding site [chemical binding]; other site 399804005816 catalytic site [active] 399804005817 metal binding site [ion binding]; metal-binding site 399804005818 carbohydrate binding site [chemical binding]; other site 399804005819 homodimer interface [polypeptide binding]; other site 399804005820 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 399804005821 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 399804005822 intersubunit interface [polypeptide binding]; other site 399804005823 active site 399804005824 Zn2+ binding site [ion binding]; other site 399804005825 L-arabinose isomerase; Provisional; Region: PRK02929 399804005826 L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose...; Region: L-fuc_L-ara-isomerases; cl00947 399804005827 hexamer (dimer of trimers) interface [polypeptide binding]; other site 399804005828 trimer interface [polypeptide binding]; other site 399804005829 substrate binding site [chemical binding]; other site 399804005830 Mn binding site [ion binding]; other site 399804005831 fructose-1-P/6-phosphogluconate phosphatase; Provisional; Region: PRK10725 399804005832 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 399804005833 active site 399804005834 motif I; other site 399804005835 motif II; other site 399804005836 Transcriptional regulators [Transcription]; Region: FadR; COG2186 399804005837 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804005838 DNA-binding site [nucleotide binding]; DNA binding site 399804005839 FCD domain; Region: FCD; pfam07729 399804005840 Glycosyl hydrolase family 43, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, alpha-L-arabinofuranosidase; Region: GH43_AXH_like; cd08990 399804005841 substrate binding site [chemical binding]; other site 399804005842 active site 399804005843 dihydroxy-acid dehydratase; Validated; Region: PRK06131 399804005844 short chain dehydrogenase; Provisional; Region: PRK12939 399804005845 classical (c) SDRs; Region: SDR_c; cd05233 399804005846 NAD(P) binding site [chemical binding]; other site 399804005847 active site 399804005848 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 399804005849 active site 399804005850 catalytic residues [active] 399804005851 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 399804005852 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 399804005853 putative ligand binding site [chemical binding]; other site 399804005854 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 399804005855 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 399804005856 Walker A/P-loop; other site 399804005857 ATP binding site [chemical binding]; other site 399804005858 Q-loop/lid; other site 399804005859 ABC transporter signature motif; other site 399804005860 Walker B; other site 399804005861 D-loop; other site 399804005862 H-loop/switch region; other site 399804005863 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 399804005864 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 399804005865 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 399804005866 TM-ABC transporter signature motif; other site 399804005867 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 399804005868 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 399804005869 TM-ABC transporter signature motif; other site 399804005870 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 399804005871 active site 399804005872 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 399804005873 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 399804005874 dimerization interface [polypeptide binding]; other site 399804005875 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804005876 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804005877 dimer interface [polypeptide binding]; other site 399804005878 putative CheW interface [polypeptide binding]; other site 399804005879 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 399804005880 active site 399804005881 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 399804005882 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 399804005883 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 399804005884 substrate binding site [chemical binding]; other site 399804005885 active site 399804005886 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 399804005887 active site 399804005888 Ricin-type beta-trefoil lectin domain-like; Region: RicinB_lectin_2; pfam14200 399804005889 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 399804005890 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 399804005891 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 399804005892 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 399804005893 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 399804005894 substrate binding site [chemical binding]; other site 399804005895 active site 399804005896 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 399804005897 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 399804005898 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 399804005899 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 399804005900 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 399804005901 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804005902 homodimer interface [polypeptide binding]; other site 399804005903 catalytic residue [active] 399804005904 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 399804005905 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 399804005906 hinge; other site 399804005907 active site 399804005908 cytidylate kinase; Provisional; Region: cmk; PRK00023 399804005909 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 399804005910 CMP-binding site; other site 399804005911 The sites determining sugar specificity; other site 399804005912 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 399804005913 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 399804005914 RNA binding site [nucleotide binding]; other site 399804005915 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 399804005916 RNA binding site [nucleotide binding]; other site 399804005917 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 399804005918 RNA binding site [nucleotide binding]; other site 399804005919 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 399804005920 RNA binding site [nucleotide binding]; other site 399804005921 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 399804005922 RNA binding site [nucleotide binding]; other site 399804005923 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 399804005924 RNA binding site [nucleotide binding]; other site 399804005925 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 399804005926 IHF dimer interface [polypeptide binding]; other site 399804005927 IHF - DNA interface [nucleotide binding]; other site 399804005928 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 399804005929 tetratricopeptide repeat protein; Provisional; Region: PRK11788 399804005930 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 399804005931 active site 399804005932 dimer interface [polypeptide binding]; other site 399804005933 short chain dehydrogenase; Provisional; Region: PRK07576 399804005934 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804005935 NAD(P) binding site [chemical binding]; other site 399804005936 active site 399804005937 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; pfam09831 399804005938 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 399804005939 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 399804005940 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 399804005941 active site 399804005942 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 399804005943 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 399804005944 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 399804005945 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 399804005946 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 399804005947 domain interface [polypeptide binding]; other site 399804005948 putative active site [active] 399804005949 catalytic site [active] 399804005950 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 399804005951 domain interface [polypeptide binding]; other site 399804005952 putative active site [active] 399804005953 catalytic site [active] 399804005954 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 399804005955 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 399804005956 putative substrate translocation pore; other site 399804005957 beta-lactamase/D-alanine carboxypeptidase; Provisional; Region: ampC; PRK11289 399804005958 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 399804005959 Uncharacterized conserved protein [Function unknown]; Region: COG3148 399804005960 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 399804005961 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 399804005962 DEAD-like helicases superfamily; Region: DEXDc; smart00487 399804005963 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 399804005964 ATP binding site [chemical binding]; other site 399804005965 putative Mg++ binding site [ion binding]; other site 399804005966 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 399804005967 nucleotide binding region [chemical binding]; other site 399804005968 ATP-binding site [chemical binding]; other site 399804005969 ecotin; Provisional; Region: PRK03719 399804005970 secondary substrate binding site; other site 399804005971 primary substrate binding site; other site 399804005972 inhibition loop; other site 399804005973 dimerization interface [polypeptide binding]; other site 399804005974 multidrug efflux protein; Reviewed; Region: PRK01766 399804005975 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 399804005976 cation binding site [ion binding]; other site 399804005977 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 399804005978 Lumazine binding domain; Region: Lum_binding; pfam00677 399804005979 Lumazine binding domain; Region: Lum_binding; pfam00677 399804005980 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 399804005981 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 399804005982 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 399804005983 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 399804005984 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 399804005985 active site 399804005986 dimer interface [polypeptide binding]; other site 399804005987 motif 1; other site 399804005988 motif 2; other site 399804005989 motif 3; other site 399804005990 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 399804005991 anticodon binding site; other site 399804005992 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 399804005993 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 399804005994 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 399804005995 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 399804005996 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 399804005997 23S rRNA binding site [nucleotide binding]; other site 399804005998 L21 binding site [polypeptide binding]; other site 399804005999 L13 binding site [polypeptide binding]; other site 399804006000 thioredoxin reductase; Provisional; Region: PRK10262 399804006001 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 399804006002 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 399804006003 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 399804006004 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 399804006005 hexamer interface [polypeptide binding]; other site 399804006006 ligand binding site [chemical binding]; other site 399804006007 putative active site [active] 399804006008 NAD(P) binding site [chemical binding]; other site 399804006009 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 399804006010 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 399804006011 putative DNA binding site [nucleotide binding]; other site 399804006012 putative Zn2+ binding site [ion binding]; other site 399804006013 AsnC family; Region: AsnC_trans_reg; pfam01037 399804006014 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 399804006015 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 399804006016 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 399804006017 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 399804006018 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 399804006019 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 399804006020 recombination factor protein RarA; Reviewed; Region: PRK13342 399804006021 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 399804006022 Walker A motif; other site 399804006023 ATP binding site [chemical binding]; other site 399804006024 Walker B motif; other site 399804006025 arginine finger; other site 399804006026 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 399804006027 camphor resistance protein CrcB; Provisional; Region: PRK14197 399804006028 seryl-tRNA synthetase; Provisional; Region: PRK05431 399804006029 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 399804006030 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 399804006031 dimer interface [polypeptide binding]; other site 399804006032 active site 399804006033 motif 1; other site 399804006034 motif 2; other site 399804006035 motif 3; other site 399804006036 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 399804006037 sulfur relay protein, TusE/DsrC/DsvC family; Region: dsrC_tusE_dsvC; TIGR03342 399804006038 sulfur relay protein TusB/DsrH; Region: sulf_tusB_dsrH; TIGR03011 399804006039 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 399804006040 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 399804006041 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 399804006042 YccA-like proteins; Region: YccA_like; cd10433 399804006043 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 399804006044 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804006045 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 399804006046 dimerization interface [polypeptide binding]; other site 399804006047 putative transporter; Provisional; Region: PRK11043 399804006048 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 399804006049 putative substrate translocation pore; other site 399804006050 Transmembrane protein 55A; Region: Tmemb_55A; pfam09788 399804006051 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 399804006052 non-specific DNA binding site [nucleotide binding]; other site 399804006053 salt bridge; other site 399804006054 sequence-specific DNA binding site [nucleotide binding]; other site 399804006055 Phage replication protein CRI; Region: Phage_CRI; pfam05144 399804006056 Phage X family; Region: Phage_X; pfam05155 399804006057 Helix-destabilising protein; Region: Phage_DNA_bind; pfam02303 399804006058 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 399804006059 Protein of unknown function (DUF3892); Region: DUF3892; pfam13031 399804006060 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 399804006061 non-specific DNA binding site [nucleotide binding]; other site 399804006062 salt bridge; other site 399804006063 sequence-specific DNA binding site [nucleotide binding]; other site 399804006064 Phage replication protein CRI; Region: Phage_CRI; pfam05144 399804006065 Phage X family; Region: Phage_X; pfam05155 399804006066 Helix-destabilising protein; Region: Phage_DNA_bind; pfam02303 399804006067 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 399804006068 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 399804006069 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 399804006070 active site 399804006071 phosphorylation site [posttranslational modification] 399804006072 intermolecular recognition site; other site 399804006073 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 399804006074 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804006075 Zn2+ binding site [ion binding]; other site 399804006076 Mg2+ binding site [ion binding]; other site 399804006077 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 399804006078 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 399804006079 Low-spin heme binding site [chemical binding]; other site 399804006080 Putative water exit pathway; other site 399804006081 Binuclear center (active site) [active] 399804006082 Putative proton exit pathway; other site 399804006083 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 399804006084 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 399804006085 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 399804006086 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 399804006087 Cytochrome c; Region: Cytochrom_C; pfam00034 399804006088 Cytochrome c; Region: Cytochrom_C; pfam00034 399804006089 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 399804006090 FixH; Region: FixH; pfam05751 399804006091 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 399804006092 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 399804006093 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 399804006094 metal-binding site [ion binding] 399804006095 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 399804006096 Soluble P-type ATPase [General function prediction only]; Region: COG4087 399804006097 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 399804006098 Family description; Region: DsbD_2; pfam13386 399804006099 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 399804006100 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 399804006101 ligand binding site [chemical binding]; other site 399804006102 flexible hinge region; other site 399804006103 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 399804006104 putative switch regulator; other site 399804006105 non-specific DNA interactions [nucleotide binding]; other site 399804006106 DNA binding site [nucleotide binding] 399804006107 sequence specific DNA binding site [nucleotide binding]; other site 399804006108 putative cAMP binding site [chemical binding]; other site 399804006109 universal stress protein UspE; Provisional; Region: PRK11175 399804006110 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 399804006111 Ligand Binding Site [chemical binding]; other site 399804006112 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 399804006113 Ligand Binding Site [chemical binding]; other site 399804006114 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 399804006115 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 399804006116 Ligand Binding Site [chemical binding]; other site 399804006117 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 399804006118 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl17361 399804006119 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 399804006120 phosphate binding site [ion binding]; other site 399804006121 putative substrate binding pocket [chemical binding]; other site 399804006122 dimer interface [polypeptide binding]; other site 399804006123 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 399804006124 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 399804006125 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804006126 homodimer interface [polypeptide binding]; other site 399804006127 catalytic residue [active] 399804006128 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 399804006129 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804006130 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 399804006131 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 399804006132 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 399804006133 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 399804006134 putative active site [active] 399804006135 Zn binding site [ion binding]; other site 399804006136 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804006137 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 399804006138 active site 399804006139 phosphorylation site [posttranslational modification] 399804006140 intermolecular recognition site; other site 399804006141 dimerization interface [polypeptide binding]; other site 399804006142 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 399804006143 DNA binding site [nucleotide binding] 399804006144 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804006145 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 399804006146 N-terminal plug; other site 399804006147 ligand-binding site [chemical binding]; other site 399804006148 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 399804006149 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 399804006150 Walker A motif; other site 399804006151 ATP binding site [chemical binding]; other site 399804006152 Walker B motif; other site 399804006153 arginine finger; other site 399804006154 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 399804006155 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 399804006156 RuvA N terminal domain; Region: RuvA_N; pfam01330 399804006157 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 399804006158 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 399804006159 active site 399804006160 putative DNA-binding cleft [nucleotide binding]; other site 399804006161 dimer interface [polypeptide binding]; other site 399804006162 hypothetical protein; Validated; Region: PRK00110 399804006163 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 399804006164 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 399804006165 dimer interface [polypeptide binding]; other site 399804006166 anticodon binding site; other site 399804006167 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 399804006168 homodimer interface [polypeptide binding]; other site 399804006169 motif 1; other site 399804006170 active site 399804006171 motif 2; other site 399804006172 GAD domain; Region: GAD; pfam02938 399804006173 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 399804006174 active site 399804006175 motif 3; other site 399804006176 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804006177 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 399804006178 substrate binding pocket [chemical binding]; other site 399804006179 membrane-bound complex binding site; other site 399804006180 hinge residues; other site 399804006181 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804006182 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 399804006183 substrate binding pocket [chemical binding]; other site 399804006184 membrane-bound complex binding site; other site 399804006185 hinge residues; other site 399804006186 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804006187 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 399804006188 substrate binding pocket [chemical binding]; other site 399804006189 membrane-bound complex binding site; other site 399804006190 hinge residues; other site 399804006191 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804006192 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804006193 metal binding site [ion binding]; metal-binding site 399804006194 active site 399804006195 I-site; other site 399804006196 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 399804006197 S-adenosylmethionine binding site [chemical binding]; other site 399804006198 Methyltransferase domain; Region: Methyltransf_23; pfam13489 399804006199 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 399804006200 S-adenosylmethionine binding site [chemical binding]; other site 399804006201 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 399804006202 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804006203 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804006204 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 399804006205 dimerization interface [polypeptide binding]; other site 399804006206 SprA-related family; Region: SprA-related; pfam12118 399804006207 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 399804006208 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 399804006209 FeS/SAM binding site; other site 399804006210 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 399804006211 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 399804006212 ThiS interaction site; other site 399804006213 putative active site [active] 399804006214 tetramer interface [polypeptide binding]; other site 399804006215 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 399804006216 thiS-thiF/thiG interaction site; other site 399804006217 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 399804006218 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 399804006219 ATP binding site [chemical binding]; other site 399804006220 substrate interface [chemical binding]; other site 399804006221 Phosphomethylpyrimidine kinase; Region: Phos_pyr_kin; pfam08543 399804006222 ATP binding site [chemical binding]; other site 399804006223 substrate binding site [chemical binding]; other site 399804006224 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 399804006225 thiamine phosphate binding site [chemical binding]; other site 399804006226 active site 399804006227 pyrophosphate binding site [ion binding]; other site 399804006228 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 399804006229 ThiC-associated domain; Region: ThiC-associated; pfam13667 399804006230 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 399804006231 Haemolysin-III related; Region: HlyIII; cl03831 399804006232 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 399804006233 DTW domain; Region: DTW; cl01221 399804006234 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_27; cd04686 399804006235 nudix motif; other site 399804006236 PAS fold; Region: PAS_4; pfam08448 399804006237 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 399804006238 putative active site [active] 399804006239 heme pocket [chemical binding]; other site 399804006240 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 399804006241 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 399804006242 putative active site [active] 399804006243 heme pocket [chemical binding]; other site 399804006244 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 399804006245 putative active site [active] 399804006246 heme pocket [chemical binding]; other site 399804006247 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804006248 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804006249 metal binding site [ion binding]; metal-binding site 399804006250 active site 399804006251 I-site; other site 399804006252 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 399804006253 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 399804006254 Family of unknown function (DUF633); Region: DUF633; pfam04816 399804006255 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 399804006256 Ligand Binding Site [chemical binding]; other site 399804006257 Helix-turn-helix domain; Region: HTH_18; pfam12833 399804006258 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804006259 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 399804006260 Uncharacterized conserved protein [Function unknown]; Region: COG2128 399804006261 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 399804006262 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 399804006263 putative RNA binding site [nucleotide binding]; other site 399804006264 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 399804006265 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2350 399804006266 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804006267 Helix-turn-helix domain; Region: HTH_18; pfam12833 399804006268 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804006269 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 399804006270 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 399804006271 transmembrane helices; other site 399804006272 Uncharacterized conserved protein [Function unknown]; Region: COG2850 399804006273 Cupin domain; Region: Cupin_2; cl17218 399804006274 Domain of unknown function (DU1801); Region: DUF1801; pfam08818 399804006275 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 399804006276 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 399804006277 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 399804006278 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 399804006279 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 399804006280 [4Fe-4S] binding site [ion binding]; other site 399804006281 molybdopterin cofactor binding site; other site 399804006282 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 399804006283 molybdopterin cofactor binding site; other site 399804006284 NapD protein; Region: NapD; pfam03927 399804006285 Periplasmic nitrate reductase protein NapE; Region: NapE; pfam06796 399804006286 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 399804006287 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 399804006288 ATP binding site [chemical binding]; other site 399804006289 putative Mg++ binding site [ion binding]; other site 399804006290 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 399804006291 nucleotide binding region [chemical binding]; other site 399804006292 ATP-binding site [chemical binding]; other site 399804006293 Helicase associated domain (HA2); Region: HA2; pfam04408 399804006294 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 399804006295 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 399804006296 FOG: CBS domain [General function prediction only]; Region: COG0517 399804006297 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 399804006298 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 399804006299 catalytic nucleophile [active] 399804006300 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 399804006301 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 399804006302 Surface antigen; Region: Bac_surface_Ag; pfam01103 399804006303 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 399804006304 Family of unknown function (DUF490); Region: DUF490; pfam04357 399804006305 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 399804006306 5S rRNA interface [nucleotide binding]; other site 399804006307 CTC domain interface [polypeptide binding]; other site 399804006308 L16 interface [polypeptide binding]; other site 399804006309 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 399804006310 Bacterial protein of unknown function (DUF882); Region: Peptidase_M15_2; pfam05951 399804006311 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 399804006312 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 399804006313 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 399804006314 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 399804006315 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 399804006316 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 399804006317 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 399804006318 Protein of unknown function (DUF2989); Region: DUF2989; pfam11207 399804006319 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 399804006320 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 399804006321 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 399804006322 quinolinate synthetase; Provisional; Region: PRK09375 399804006323 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 399804006324 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 399804006325 E3 interaction surface; other site 399804006326 lipoyl attachment site [posttranslational modification]; other site 399804006327 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 399804006328 E3 interaction surface; other site 399804006329 lipoyl attachment site [posttranslational modification]; other site 399804006330 e3 binding domain; Region: E3_binding; pfam02817 399804006331 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 399804006332 3-methyl-2-oxobutanate dehydrogenase; Provisional; Region: PTZ00182 399804006333 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 399804006334 alpha subunit interface [polypeptide binding]; other site 399804006335 TPP binding site [chemical binding]; other site 399804006336 heterodimer interface [polypeptide binding]; other site 399804006337 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 399804006338 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 399804006339 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 399804006340 tetramer interface [polypeptide binding]; other site 399804006341 TPP-binding site [chemical binding]; other site 399804006342 heterodimer interface [polypeptide binding]; other site 399804006343 phosphorylation loop region [posttranslational modification] 399804006344 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 399804006345 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 399804006346 putative active site [active] 399804006347 Zn binding site [ion binding]; other site 399804006348 methionine sulfoxide reductase A; Provisional; Region: PRK14054 399804006349 phosphoglucomutase; Validated; Region: PRK07564 399804006350 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 399804006351 active site 399804006352 substrate binding site [chemical binding]; other site 399804006353 metal binding site [ion binding]; metal-binding site 399804006354 SeqA protein; Region: SeqA; pfam03925 399804006355 acyl-CoA esterase; Provisional; Region: PRK10673 399804006356 PGAP1-like protein; Region: PGAP1; pfam07819 399804006357 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 399804006358 LexA regulated protein; Provisional; Region: PRK11675 399804006359 flavodoxin FldA; Validated; Region: PRK09267 399804006360 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 399804006361 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 399804006362 elongation factor P; Validated; Region: PRK00529 399804006363 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 399804006364 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 399804006365 RNA binding site [nucleotide binding]; other site 399804006366 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 399804006367 RNA binding site [nucleotide binding]; other site 399804006368 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 399804006369 aminotransferase AlaT; Validated; Region: PRK09265 399804006370 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 399804006371 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804006372 homodimer interface [polypeptide binding]; other site 399804006373 catalytic residue [active] 399804006374 5'-nucleotidase; Provisional; Region: PRK03826 399804006375 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 399804006376 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 399804006377 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 399804006378 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 399804006379 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 399804006380 active site 399804006381 intersubunit interface [polypeptide binding]; other site 399804006382 catalytic residue [active] 399804006383 phosphogluconate dehydratase; Validated; Region: PRK09054 399804006384 6-phosphogluconate dehydratase; Region: edd; TIGR01196 399804006385 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 399804006386 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 399804006387 putative active site [active] 399804006388 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 399804006389 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 399804006390 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 399804006391 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 399804006392 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 399804006393 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 399804006394 putative active site [active] 399804006395 pyruvate kinase; Provisional; Region: PRK05826 399804006396 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 399804006397 domain interfaces; other site 399804006398 active site 399804006399 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804006400 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 399804006401 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 399804006402 active site 399804006403 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 399804006404 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804006405 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804006406 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 399804006407 Smr domain; Region: Smr; pfam01713 399804006408 SnoaL-like domain; Region: SnoaL_3; pfam13474 399804006409 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 399804006410 SEC-C motif; Region: SEC-C; pfam02810 399804006411 SEC-C motif; Region: SEC-C; pfam02810 399804006412 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 399804006413 GAF domain; Region: GAF; pfam01590 399804006414 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 399804006415 PAS fold; Region: PAS_3; pfam08447 399804006416 putative active site [active] 399804006417 heme pocket [chemical binding]; other site 399804006418 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804006419 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804006420 metal binding site [ion binding]; metal-binding site 399804006421 active site 399804006422 I-site; other site 399804006423 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 399804006424 Protein of unknown function (DUF406); Region: DUF406; pfam04175 399804006425 Ribosomal S4P (gammaproteobacterial); Region: Ribosomal_S4Pg; pfam11993 399804006426 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 399804006427 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 399804006428 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 399804006429 Ligand Binding Site [chemical binding]; other site 399804006430 rhomboid family GlyGly-CTERM serine protease; Region: rhom_GG_sort; TIGR03902 399804006431 excinuclease ABC subunit B; Provisional; Region: PRK05298 399804006432 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 399804006433 ATP binding site [chemical binding]; other site 399804006434 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 399804006435 nucleotide binding region [chemical binding]; other site 399804006436 ATP-binding site [chemical binding]; other site 399804006437 Ultra-violet resistance protein B; Region: UvrB; pfam12344 399804006438 UvrB/uvrC motif; Region: UVR; pfam02151 399804006439 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804006440 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804006441 active site 399804006442 I-site; other site 399804006443 metal binding site [ion binding]; metal-binding site 399804006444 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 399804006445 electron transport complex protein RsxA; Provisional; Region: PRK05151 399804006446 ferredoxin; Provisional; Region: PRK08764 399804006447 Putative Fe-S cluster; Region: FeS; pfam04060 399804006448 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 399804006449 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 399804006450 SLBB domain; Region: SLBB; pfam10531 399804006451 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 399804006452 electron transport complex protein RnfD; Reviewed; Region: rnfD; PRK00816 399804006453 electron transport complex protein RnfG; Validated; Region: PRK01908 399804006454 electron transport complex RsxE subunit; Provisional; Region: PRK12405 399804006455 endonuclease III; Provisional; Region: PRK10702 399804006456 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 399804006457 minor groove reading motif; other site 399804006458 helix-hairpin-helix signature motif; other site 399804006459 substrate binding pocket [chemical binding]; other site 399804006460 active site 399804006461 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 399804006462 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 399804006463 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 399804006464 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 399804006465 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 399804006466 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 399804006467 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 399804006468 N-terminal plug; other site 399804006469 ligand-binding site [chemical binding]; other site 399804006470 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 399804006471 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804006472 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804006473 ABC transporter; Region: ABC_tran_2; pfam12848 399804006474 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804006475 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 399804006476 CoA binding domain; Region: CoA_binding_2; pfam13380 399804006477 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 399804006478 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 399804006479 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 399804006480 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 399804006481 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 399804006482 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 399804006483 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 399804006484 dimerization interface [polypeptide binding]; other site 399804006485 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 399804006486 ATP binding site [chemical binding]; other site 399804006487 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 399804006488 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 399804006489 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 399804006490 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 399804006491 putative acyl-acceptor binding pocket; other site 399804006492 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 399804006493 IHF dimer interface [polypeptide binding]; other site 399804006494 IHF - DNA interface [nucleotide binding]; other site 399804006495 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 399804006496 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 399804006497 putative tRNA-binding site [nucleotide binding]; other site 399804006498 B3/4 domain; Region: B3_4; pfam03483 399804006499 tRNA synthetase B5 domain; Region: B5; smart00874 399804006500 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 399804006501 dimer interface [polypeptide binding]; other site 399804006502 motif 1; other site 399804006503 motif 3; other site 399804006504 motif 2; other site 399804006505 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 399804006506 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 399804006507 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 399804006508 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 399804006509 dimer interface [polypeptide binding]; other site 399804006510 motif 1; other site 399804006511 active site 399804006512 motif 2; other site 399804006513 motif 3; other site 399804006514 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804006515 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804006516 dimer interface [polypeptide binding]; other site 399804006517 putative CheW interface [polypeptide binding]; other site 399804006518 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 399804006519 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 399804006520 N-terminal plug; other site 399804006521 ligand-binding site [chemical binding]; other site 399804006522 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 399804006523 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 399804006524 DEAD/DEAH box helicase; Region: DEAD; pfam00270 399804006525 DEAD_2; Region: DEAD_2; pfam06733 399804006526 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 399804006527 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 399804006528 CRISPR/Cas system-associated protein Cas3/Cas2; Region: Cas3_Cas2_I-F; cd09673 399804006529 CRISPR-associated endonuclease Cas3-HD; Region: cas3_HD; TIGR01596 399804006530 DEAD-like helicases superfamily; Region: DEXDc; smart00487 399804006531 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 399804006532 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 399804006533 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 399804006534 Beta-lactamase; Region: Beta-lactamase; pfam00144 399804006535 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 399804006536 Major Facilitator Superfamily; Region: MFS_1; pfam07690 399804006537 putative substrate translocation pore; other site 399804006538 Nitrate and nitrite sensing; Region: NIT; pfam08376 399804006539 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 399804006540 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804006541 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804006542 dimer interface [polypeptide binding]; other site 399804006543 putative CheW interface [polypeptide binding]; other site 399804006544 hypothetical protein; Provisional; Region: PRK11111 399804006545 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 399804006546 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 399804006547 putative catalytic cysteine [active] 399804006548 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 399804006549 putative active site [active] 399804006550 metal binding site [ion binding]; metal-binding site 399804006551 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 399804006552 putative active site [active] 399804006553 Zn binding site [ion binding]; other site 399804006554 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 399804006555 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804006556 Coenzyme A binding pocket [chemical binding]; other site 399804006557 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 399804006558 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804006559 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804006560 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 399804006561 Fumarase C-terminus; Region: Fumerase_C; pfam05683 399804006562 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 399804006563 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 399804006564 chorismate binding enzyme; Region: Chorismate_bind; cl10555 399804006565 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 399804006566 putative active site [active] 399804006567 putative CoA binding site [chemical binding]; other site 399804006568 nudix motif; other site 399804006569 metal binding site [ion binding]; metal-binding site 399804006570 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 399804006571 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 399804006572 putative dimer interface [polypeptide binding]; other site 399804006573 putative anticodon binding site; other site 399804006574 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 399804006575 homodimer interface [polypeptide binding]; other site 399804006576 motif 1; other site 399804006577 motif 2; other site 399804006578 active site 399804006579 motif 3; other site 399804006580 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804006581 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 399804006582 substrate binding pocket [chemical binding]; other site 399804006583 membrane-bound complex binding site; other site 399804006584 hinge residues; other site 399804006585 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 399804006586 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 399804006587 ATP-grasp domain; Region: ATP-grasp_4; cl17255 399804006588 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 399804006589 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 399804006590 PAS domain; Region: PAS_9; pfam13426 399804006591 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804006592 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804006593 metal binding site [ion binding]; metal-binding site 399804006594 active site 399804006595 I-site; other site 399804006596 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 399804006597 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 399804006598 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 399804006599 S-adenosylmethionine binding site [chemical binding]; other site 399804006600 Domain of unknown function (DUF4274); Region: DUF4274; pfam14096 399804006601 rhombotail lipoprotein; Region: rhombo_lipo; TIGR04179 399804006602 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 399804006603 active site 399804006604 catalytic residues [active] 399804006605 metal binding site [ion binding]; metal-binding site 399804006606 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 399804006607 active site 399804006608 DNA binding site [nucleotide binding] 399804006609 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 399804006610 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 399804006611 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 399804006612 putative active site [active] 399804006613 putative dimer interface [polypeptide binding]; other site 399804006614 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 399804006615 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 399804006616 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 399804006617 active site 399804006618 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 399804006619 PRC-barrel domain; Region: PRC; pfam05239 399804006620 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 399804006621 BON domain; Region: BON; pfam04972 399804006622 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 399804006623 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; cl00047 399804006624 ligand binding site [chemical binding]; other site 399804006625 flexible hinge region; other site 399804006626 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 399804006627 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 399804006628 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 399804006629 ligand binding site [chemical binding]; other site 399804006630 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 399804006631 outer membrane lipoprotein; Provisional; Region: PRK11023 399804006632 BON domain; Region: BON; pfam04972 399804006633 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 399804006634 BON domain; Region: BON; pfam04972 399804006635 BON domain; Region: BON; pfam04972 399804006636 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 399804006637 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 399804006638 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804006639 ligand binding site [chemical binding]; other site 399804006640 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 399804006641 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 399804006642 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 399804006643 quinone interaction residues [chemical binding]; other site 399804006644 active site 399804006645 catalytic residues [active] 399804006646 FMN binding site [chemical binding]; other site 399804006647 substrate binding site [chemical binding]; other site 399804006648 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 399804006649 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 399804006650 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 399804006651 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 399804006652 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 399804006653 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 399804006654 aminopeptidase N; Provisional; Region: pepN; PRK14015 399804006655 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 399804006656 active site 399804006657 Zn binding site [ion binding]; other site 399804006658 carboxy-terminal protease; Provisional; Region: PRK11186 399804006659 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 399804006660 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 399804006661 protein binding site [polypeptide binding]; other site 399804006662 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 399804006663 Catalytic dyad [active] 399804006664 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 399804006665 ProP expression regulator; Provisional; Region: PRK04950 399804006666 ProQ/FINO family; Region: ProQ; smart00945 399804006667 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 399804006668 GAF domain; Region: GAF_2; pfam13185 399804006669 YebG protein; Region: YebG; pfam07130 399804006670 Paraquat-inducible protein A; Region: PqiA; pfam04403 399804006671 Paraquat-inducible protein A; Region: PqiA; pfam04403 399804006672 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 399804006673 mce related protein; Region: MCE; pfam02470 399804006674 mce related protein; Region: MCE; pfam02470 399804006675 mce related protein; Region: MCE; pfam02470 399804006676 mce related protein; Region: MCE; pfam02470 399804006677 mce related protein; Region: MCE; pfam02470 399804006678 mce related protein; Region: MCE; pfam02470 399804006679 mce related protein; Region: MCE; pfam02470 399804006680 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 399804006681 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 399804006682 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 399804006683 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 399804006684 S-adenosylmethionine binding site [chemical binding]; other site 399804006685 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 399804006686 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 399804006687 active site 399804006688 PilZ domain; Region: PilZ; cl01260 399804006689 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 399804006690 DNA polymerase III subunit delta'; Validated; Region: PRK08485 399804006691 ATPase involved in DNA replication [DNA replication, recombination, and repair]; Region: HolB; COG0470 399804006692 thymidylate kinase; Validated; Region: tmk; PRK00698 399804006693 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 399804006694 TMP-binding site; other site 399804006695 ATP-binding site [chemical binding]; other site 399804006696 YceG-like family; Region: YceG; pfam02618 399804006697 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 399804006698 dimerization interface [polypeptide binding]; other site 399804006699 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 399804006700 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 399804006701 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804006702 catalytic residue [active] 399804006703 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 399804006704 trimer interface [polypeptide binding]; other site 399804006705 active site 399804006706 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 399804006707 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 399804006708 Sugar specificity; other site 399804006709 Pyrimidine base specificity; other site 399804006710 ATP-binding site [chemical binding]; other site 399804006711 antiporter inner membrane protein; Provisional; Region: PRK11670 399804006712 Domain of unknown function DUF59; Region: DUF59; cl00941 399804006713 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 399804006714 Walker A motif; other site 399804006715 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 399804006716 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 399804006717 active site 399804006718 HIGH motif; other site 399804006719 KMSKS motif; other site 399804006720 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 399804006721 tRNA binding surface [nucleotide binding]; other site 399804006722 anticodon binding site; other site 399804006723 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 399804006724 dimer interface [polypeptide binding]; other site 399804006725 putative tRNA-binding site [nucleotide binding]; other site 399804006726 Predicted permeases [General function prediction only]; Region: COG0679 399804006727 Uncharacterized conserved protein [Function unknown]; Region: COG0327 399804006728 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 399804006729 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 399804006730 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 399804006731 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 399804006732 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 399804006733 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 399804006734 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 399804006735 rRNA binding site [nucleotide binding]; other site 399804006736 predicted 30S ribosome binding site; other site 399804006737 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 399804006738 Clp amino terminal domain; Region: Clp_N; pfam02861 399804006739 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 399804006740 Walker A motif; other site 399804006741 ATP binding site [chemical binding]; other site 399804006742 Walker B motif; other site 399804006743 arginine finger; other site 399804006744 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 399804006745 Walker A motif; other site 399804006746 ATP binding site [chemical binding]; other site 399804006747 Walker B motif; other site 399804006748 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 399804006749 Uncharacterized conserved protein [Function unknown]; Region: COG2127 399804006750 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 399804006751 DNA-binding site [nucleotide binding]; DNA binding site 399804006752 RNA-binding motif; other site 399804006753 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 399804006754 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 399804006755 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 399804006756 pseudouridine synthase; Region: TIGR00093 399804006757 probable active site [active] 399804006758 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 399804006759 nudix motif; other site 399804006760 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 399804006761 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 399804006762 putative lysogenization regulator; Reviewed; Region: PRK00218 399804006763 adenylosuccinate lyase; Provisional; Region: PRK09285 399804006764 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 399804006765 tetramer interface [polypeptide binding]; other site 399804006766 active site 399804006767 Cupin superfamily protein; Region: Cupin_4; pfam08007 399804006768 Cupin-like domain; Region: Cupin_8; pfam13621 399804006769 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 399804006770 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 399804006771 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 399804006772 NAD binding site [chemical binding]; other site 399804006773 Phe binding site; other site 399804006774 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 399804006775 MarR family; Region: MarR; pfam01047 399804006776 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 399804006777 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 399804006778 FAD binding domain; Region: FAD_binding_4; pfam01565 399804006779 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 399804006780 phosphoenolpyruvate synthase; Validated; Region: PRK06464 399804006781 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 399804006782 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 399804006783 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 399804006784 PEP synthetase regulatory protein; Provisional; Region: PRK05339 399804006785 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12756 399804006786 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 399804006787 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 399804006788 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 399804006789 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 399804006790 active site 399804006791 phosphorylation site [posttranslational modification] 399804006792 intermolecular recognition site; other site 399804006793 dimerization interface [polypeptide binding]; other site 399804006794 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 399804006795 DNA binding residues [nucleotide binding] 399804006796 dimerization interface [polypeptide binding]; other site 399804006797 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 399804006798 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804006799 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 399804006800 substrate binding site [chemical binding]; other site 399804006801 dimerization interface [polypeptide binding]; other site 399804006802 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 399804006803 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 399804006804 active site 399804006805 interdomain interaction site; other site 399804006806 putative metal-binding site [ion binding]; other site 399804006807 nucleotide binding site [chemical binding]; other site 399804006808 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 399804006809 domain I; other site 399804006810 DNA binding groove [nucleotide binding] 399804006811 phosphate binding site [ion binding]; other site 399804006812 domain II; other site 399804006813 domain III; other site 399804006814 nucleotide binding site [chemical binding]; other site 399804006815 catalytic site [active] 399804006816 domain IV; other site 399804006817 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 399804006818 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 399804006819 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 399804006820 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 399804006821 succinylarginine dihydrolase; Provisional; Region: PRK13281 399804006822 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 399804006823 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 399804006824 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 399804006825 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 399804006826 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 399804006827 active site 399804006828 phosphorylation site [posttranslational modification] 399804006829 intermolecular recognition site; other site 399804006830 dimerization interface [polypeptide binding]; other site 399804006831 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 399804006832 DNA binding site [nucleotide binding] 399804006833 sensor protein PhoQ; Provisional; Region: PRK10815 399804006834 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 399804006835 ATP binding site [chemical binding]; other site 399804006836 Mg2+ binding site [ion binding]; other site 399804006837 G-X-G motif; other site 399804006838 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; cl17304 399804006839 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 399804006840 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 399804006841 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804006842 Zn2+ binding site [ion binding]; other site 399804006843 Mg2+ binding site [ion binding]; other site 399804006844 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 399804006845 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 399804006846 Cl binding site [ion binding]; other site 399804006847 oligomer interface [polypeptide binding]; other site 399804006848 AAA domain; Region: AAA_33; pfam13671 399804006849 NAD-dependent deacetylase; Provisional; Region: PRK00481 399804006850 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 399804006851 NAD+ binding site [chemical binding]; other site 399804006852 substrate binding site [chemical binding]; other site 399804006853 Zn binding site [ion binding]; other site 399804006854 ferric uptake regulator; Provisional; Region: fur; PRK09462 399804006855 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 399804006856 metal binding site 2 [ion binding]; metal-binding site 399804006857 putative DNA binding helix; other site 399804006858 metal binding site 1 [ion binding]; metal-binding site 399804006859 dimer interface [polypeptide binding]; other site 399804006860 structural Zn2+ binding site [ion binding]; other site 399804006861 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 399804006862 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 399804006863 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 399804006864 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 399804006865 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804006866 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 399804006867 CoA binding domain; Region: CoA_binding; pfam02629 399804006868 CoA-ligase; Region: Ligase_CoA; pfam00549 399804006869 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 399804006870 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 399804006871 CoA-ligase; Region: Ligase_CoA; pfam00549 399804006872 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 399804006873 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 399804006874 E3 interaction surface; other site 399804006875 lipoyl attachment site [posttranslational modification]; other site 399804006876 e3 binding domain; Region: E3_binding; pfam02817 399804006877 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 399804006878 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 399804006879 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 399804006880 TPP-binding site [chemical binding]; other site 399804006881 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 399804006882 PYR/PP interface [polypeptide binding]; other site 399804006883 dimer interface [polypeptide binding]; other site 399804006884 TPP binding site [chemical binding]; other site 399804006885 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 399804006886 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 399804006887 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 399804006888 L-aspartate oxidase; Provisional; Region: PRK06175 399804006889 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 399804006890 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 399804006891 SdhC subunit interface [polypeptide binding]; other site 399804006892 proximal heme binding site [chemical binding]; other site 399804006893 cardiolipin binding site; other site 399804006894 Iron-sulfur protein interface; other site 399804006895 proximal quinone binding site [chemical binding]; other site 399804006896 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 399804006897 Iron-sulfur protein interface; other site 399804006898 proximal quinone binding site [chemical binding]; other site 399804006899 SdhD (CybS) interface [polypeptide binding]; other site 399804006900 proximal heme binding site [chemical binding]; other site 399804006901 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 399804006902 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 399804006903 dimer interface [polypeptide binding]; other site 399804006904 active site 399804006905 citrylCoA binding site [chemical binding]; other site 399804006906 NADH binding [chemical binding]; other site 399804006907 cationic pore residues; other site 399804006908 oxalacetate/citrate binding site [chemical binding]; other site 399804006909 coenzyme A binding site [chemical binding]; other site 399804006910 catalytic triad [active] 399804006911 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804006912 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 399804006913 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804006914 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 399804006915 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804006916 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804006917 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 399804006918 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 399804006919 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 399804006920 Ion transport protein; Region: Ion_trans; pfam00520 399804006921 Ion channel; Region: Ion_trans_2; pfam07885 399804006922 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 399804006923 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_4; cd07268 399804006924 putative metal binding site [ion binding]; other site 399804006925 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 399804006926 Peptidase family M23; Region: Peptidase_M23; pfam01551 399804006927 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 399804006928 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 399804006929 Nucleoid-associated protein [General function prediction only]; Region: COG3081 399804006930 nucleoid-associated protein NdpA; Validated; Region: PRK00378 399804006931 hypothetical protein; Provisional; Region: PRK13689 399804006932 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 399804006933 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 399804006934 Sulfatase; Region: Sulfatase; cl17466 399804006935 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 399804006936 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 399804006937 active site 399804006938 FMN binding site [chemical binding]; other site 399804006939 substrate binding site [chemical binding]; other site 399804006940 homotetramer interface [polypeptide binding]; other site 399804006941 catalytic residue [active] 399804006942 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804006943 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804006944 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 399804006945 dimerization interface [polypeptide binding]; other site 399804006946 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 399804006947 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 399804006948 homodimer interface [polypeptide binding]; other site 399804006949 NAD binding pocket [chemical binding]; other site 399804006950 ATP binding pocket [chemical binding]; other site 399804006951 Mg binding site [ion binding]; other site 399804006952 active-site loop [active] 399804006953 inosine/guanosine kinase; Provisional; Region: PRK15074 399804006954 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 399804006955 substrate binding site [chemical binding]; other site 399804006956 ATP binding site [chemical binding]; other site 399804006957 ferrochelatase; Reviewed; Region: hemH; PRK00035 399804006958 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 399804006959 C-terminal domain interface [polypeptide binding]; other site 399804006960 active site 399804006961 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 399804006962 active site 399804006963 N-terminal domain interface [polypeptide binding]; other site 399804006964 adenylate kinase; Reviewed; Region: adk; PRK00279 399804006965 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 399804006966 AMP-binding site [chemical binding]; other site 399804006967 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 399804006968 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 399804006969 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 399804006970 heat shock protein 90; Provisional; Region: PRK05218 399804006971 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 399804006972 ATP binding site [chemical binding]; other site 399804006973 Mg2+ binding site [ion binding]; other site 399804006974 G-X-G motif; other site 399804006975 recombination protein RecR; Reviewed; Region: recR; PRK00076 399804006976 RecR protein; Region: RecR; pfam02132 399804006977 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 399804006978 putative active site [active] 399804006979 putative metal-binding site [ion binding]; other site 399804006980 tetramer interface [polypeptide binding]; other site 399804006981 hypothetical protein; Validated; Region: PRK00153 399804006982 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14949 399804006983 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 399804006984 Walker A motif; other site 399804006985 ATP binding site [chemical binding]; other site 399804006986 Walker B motif; other site 399804006987 DNA polymerase III subunit delta'; Validated; Region: PRK08485 399804006988 arginine finger; other site 399804006989 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 399804006990 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 399804006991 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 399804006992 active site 399804006993 hypothetical protein; Provisional; Region: PRK10527 399804006994 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 399804006995 hypothetical protein; Provisional; Region: PRK05409 399804006996 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 399804006997 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 399804006998 FMN binding site [chemical binding]; other site 399804006999 active site 399804007000 catalytic residues [active] 399804007001 substrate binding site [chemical binding]; other site 399804007002 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 399804007003 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 399804007004 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 399804007005 active site 399804007006 metal binding site [ion binding]; metal-binding site 399804007007 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 399804007008 putative hydrolase; Provisional; Region: PRK11460 399804007009 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 399804007010 Protein of unknown function (DUF3389); Region: DUF3389; pfam11869 399804007011 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 399804007012 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 399804007013 active site 399804007014 Zn binding site [ion binding]; other site 399804007015 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 399804007016 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 399804007017 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804007018 Transglycosylase SLT domain; Region: SLT_2; pfam13406 399804007019 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 399804007020 N-acetyl-D-glucosamine binding site [chemical binding]; other site 399804007021 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 399804007022 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 399804007023 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 399804007024 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 399804007025 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 399804007026 active site 399804007027 phosphorylation site [posttranslational modification] 399804007028 intermolecular recognition site; other site 399804007029 dimerization interface [polypeptide binding]; other site 399804007030 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 399804007031 S-adenosylmethionine binding site [chemical binding]; other site 399804007032 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 399804007033 RNA polymerase sigma factor; Provisional; Region: PRK11924 399804007034 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 399804007035 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 399804007036 DNA binding residues [nucleotide binding] 399804007037 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 399804007038 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 399804007039 putative nicotinate phosphoribosyltransferase; Provisional; Region: PRK09198 399804007040 pre-B-cell colony-enhancing factor (PBEF)-like. The mammalian members of this group of nicotinate phosphoribosyltransferases (NAPRTases) were originally identified as genes whose expression is upregulated upon activation in lymphoid cells. In general; Region: PBEF_like; cd01569 399804007041 active site 399804007042 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 399804007043 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 399804007044 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 399804007045 active site 399804007046 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 399804007047 nudix motif; other site 399804007048 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 399804007049 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 399804007050 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 399804007051 hypothetical protein; Provisional; Region: PRK11770 399804007052 Domain of unknown function (DUF307); Region: DUF307; pfam03733 399804007053 Domain of unknown function (DUF307); Region: DUF307; pfam03733 399804007054 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 399804007055 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 399804007056 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 399804007057 DNA binding residues [nucleotide binding] 399804007058 dimerization interface [polypeptide binding]; other site 399804007059 heat shock protein HtpX; Provisional; Region: PRK05457 399804007060 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 399804007061 active site pocket [active] 399804007062 oxyanion hole [active] 399804007063 catalytic triad [active] 399804007064 active site nucleophile [active] 399804007065 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 399804007066 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 399804007067 Protein of unknown function (DUF3187); Region: DUF3187; pfam11383 399804007068 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 399804007069 Uncharacterized conserved protein (DUF2149); Region: DUF2149; pfam09919 399804007070 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 399804007071 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 399804007072 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804007073 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 399804007074 N-terminal plug; other site 399804007075 ligand-binding site [chemical binding]; other site 399804007076 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 399804007077 AAA domain; Region: AAA_26; pfam13500 399804007078 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 399804007079 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 399804007080 S-adenosylmethionine binding site [chemical binding]; other site 399804007081 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 399804007082 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 399804007083 substrate-cofactor binding pocket; other site 399804007084 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804007085 catalytic residue [active] 399804007086 biotin synthase; Provisional; Region: PRK15108 399804007087 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 399804007088 FeS/SAM binding site; other site 399804007089 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 399804007090 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 399804007091 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 399804007092 inhibitor-cofactor binding pocket; inhibition site 399804007093 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804007094 catalytic residue [active] 399804007095 Cache domain; Region: Cache_2; cl07034 399804007096 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 399804007097 dimerization interface [polypeptide binding]; other site 399804007098 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804007099 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804007100 dimer interface [polypeptide binding]; other site 399804007101 putative CheW interface [polypeptide binding]; other site 399804007102 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 399804007103 Na binding site [ion binding]; other site 399804007104 PAS domain; Region: PAS; smart00091 399804007105 PAS fold; Region: PAS_7; pfam12860 399804007106 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804007107 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 399804007108 dimer interface [polypeptide binding]; other site 399804007109 phosphorylation site [posttranslational modification] 399804007110 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 399804007111 ATP binding site [chemical binding]; other site 399804007112 Mg2+ binding site [ion binding]; other site 399804007113 G-X-G motif; other site 399804007114 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 399804007115 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 399804007116 active site 399804007117 phosphorylation site [posttranslational modification] 399804007118 intermolecular recognition site; other site 399804007119 dimerization interface [polypeptide binding]; other site 399804007120 acetyl-CoA synthetase; Provisional; Region: PRK00174 399804007121 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 399804007122 active site 399804007123 CoA binding site [chemical binding]; other site 399804007124 acyl-activating enzyme (AAE) consensus motif; other site 399804007125 AMP binding site [chemical binding]; other site 399804007126 acetate binding site [chemical binding]; other site 399804007127 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 399804007128 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 399804007129 ATP binding site [chemical binding]; other site 399804007130 putative Mg++ binding site [ion binding]; other site 399804007131 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 399804007132 nucleotide binding region [chemical binding]; other site 399804007133 ATP-binding site [chemical binding]; other site 399804007134 Double zinc ribbon; Region: DZR; pfam12773 399804007135 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 399804007136 GSH binding site [chemical binding]; other site 399804007137 catalytic residues [active] 399804007138 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 399804007139 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 399804007140 active site 399804007141 motif I; other site 399804007142 motif II; other site 399804007143 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 399804007144 Transcriptional regulators [Transcription]; Region: GntR; COG1802 399804007145 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804007146 DNA-binding site [nucleotide binding]; DNA binding site 399804007147 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 399804007148 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 399804007149 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 399804007150 dimer interface [polypeptide binding]; other site 399804007151 active site 399804007152 CoA binding pocket [chemical binding]; other site 399804007153 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 399804007154 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 399804007155 active site 399804007156 catalytic site [active] 399804007157 substrate binding site [chemical binding]; other site 399804007158 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 399804007159 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 399804007160 ligand binding site [chemical binding]; other site 399804007161 flexible hinge region; other site 399804007162 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 399804007163 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 399804007164 metal binding triad; other site 399804007165 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 399804007166 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 399804007167 Na binding site [ion binding]; other site 399804007168 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 399804007169 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 399804007170 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 399804007171 catalytic residues [active] 399804007172 hinge region; other site 399804007173 alpha helical domain; other site 399804007174 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 399804007175 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 399804007176 putative NAD(P) binding site [chemical binding]; other site 399804007177 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 399804007178 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 399804007179 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804007180 Zn2+ binding site [ion binding]; other site 399804007181 Mg2+ binding site [ion binding]; other site 399804007182 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 399804007183 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 399804007184 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 399804007185 nucleotide binding pocket [chemical binding]; other site 399804007186 K-X-D-G motif; other site 399804007187 catalytic site [active] 399804007188 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 399804007189 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 399804007190 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 399804007191 Dimer interface [polypeptide binding]; other site 399804007192 BRCT sequence motif; other site 399804007193 cell division protein ZipA; Provisional; Region: PRK03427 399804007194 ZipA, C-terminal FtsZ-binding domain; Region: ZipA_C; pfam04354 399804007195 FtsZ protein binding site [polypeptide binding]; other site 399804007196 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 399804007197 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 399804007198 Walker A/P-loop; other site 399804007199 ATP binding site [chemical binding]; other site 399804007200 Q-loop/lid; other site 399804007201 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 399804007202 ABC transporter signature motif; other site 399804007203 Walker B; other site 399804007204 D-loop; other site 399804007205 H-loop/switch region; other site 399804007206 putative sulfate transport protein CysZ; Validated; Region: PRK04949 399804007207 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 399804007208 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 399804007209 active site 399804007210 RDD family; Region: RDD; pfam06271 399804007211 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 399804007212 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 399804007213 dimer interface [polypeptide binding]; other site 399804007214 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804007215 catalytic residue [active] 399804007216 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804007217 C-20 methyltransferase BchU; Region: C20_methyl_CrtF; TIGR02716 399804007218 O-methyltransferase; Region: Methyltransf_2; pfam00891 399804007219 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 399804007220 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 399804007221 gating phenylalanine in ion channel; other site 399804007222 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 399804007223 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 399804007224 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 399804007225 hypothetical protein; Provisional; Region: PRK11588 399804007226 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 399804007227 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 399804007228 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804007229 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 399804007230 putative dimerization interface [polypeptide binding]; other site 399804007231 formate transporter FocA; Region: formate_focA; TIGR04060 399804007232 FOG: CBS domain [General function prediction only]; Region: COG0517 399804007233 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 399804007234 CBS domain; Region: CBS; pfam00571 399804007235 FOG: CBS domain [General function prediction only]; Region: COG0517 399804007236 Protein of unknown function (DUF3360); Region: DUF3360; pfam11840 399804007237 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 399804007238 Pyruvate formate lyase 1; Region: PFL1; cd01678 399804007239 coenzyme A binding site [chemical binding]; other site 399804007240 active site 399804007241 catalytic residues [active] 399804007242 glycine loop; other site 399804007243 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 399804007244 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 399804007245 FeS/SAM binding site; other site 399804007246 Protein of unknown function, DUF412; Region: DUF412; pfam04217 399804007247 propionate/acetate kinase; Provisional; Region: PRK12379 399804007248 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 399804007249 phosphate acetyltransferase; Reviewed; Region: PRK05632 399804007250 DRTGG domain; Region: DRTGG; pfam07085 399804007251 phosphate acetyltransferase; Region: pta; TIGR00651 399804007252 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 399804007253 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 399804007254 S-adenosylmethionine binding site [chemical binding]; other site 399804007255 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 399804007256 Domain of unknown function DUF20; Region: UPF0118; pfam01594 399804007257 D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase; Provisional; Region: folX; PRK11245 399804007258 active site 399804007259 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 399804007260 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 399804007261 putative NAD(P) binding site [chemical binding]; other site 399804007262 putative active site [active] 399804007263 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 399804007264 FtsX-like permease family; Region: FtsX; pfam02687 399804007265 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 399804007266 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 399804007267 Walker A/P-loop; other site 399804007268 ATP binding site [chemical binding]; other site 399804007269 Q-loop/lid; other site 399804007270 ABC transporter signature motif; other site 399804007271 Walker B; other site 399804007272 D-loop; other site 399804007273 H-loop/switch region; other site 399804007274 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 399804007275 active site 399804007276 catalytic triad [active] 399804007277 oxyanion hole [active] 399804007278 switch loop; other site 399804007279 Protein of unknown function (DUF3083); Region: DUF3083; pfam11281 399804007280 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 399804007281 putative inner membrane peptidase; Provisional; Region: PRK11778 399804007282 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 399804007283 tandem repeat interface [polypeptide binding]; other site 399804007284 oligomer interface [polypeptide binding]; other site 399804007285 active site residues [active] 399804007286 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 399804007287 Bacterial virulence factor lipase N-terminal; Region: Lipase_bact_N; pfam12262 399804007288 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 399804007289 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804007290 NAD(P) binding site [chemical binding]; other site 399804007291 active site 399804007292 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804007293 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 399804007294 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 399804007295 RNA binding surface [nucleotide binding]; other site 399804007296 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 399804007297 probable active site [active] 399804007298 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 399804007299 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 399804007300 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 399804007301 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 399804007302 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 399804007303 active site 399804007304 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 399804007305 anthranilate synthase component I; Provisional; Region: PRK13564 399804007306 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 399804007307 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 399804007308 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 399804007309 glutamine binding [chemical binding]; other site 399804007310 catalytic triad [active] 399804007311 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 399804007312 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 399804007313 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 399804007314 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 399804007315 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 399804007316 active site 399804007317 ribulose/triose binding site [chemical binding]; other site 399804007318 phosphate binding site [ion binding]; other site 399804007319 substrate (anthranilate) binding pocket [chemical binding]; other site 399804007320 product (indole) binding pocket [chemical binding]; other site 399804007321 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 399804007322 active site 399804007323 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 399804007324 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 399804007325 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804007326 catalytic residue [active] 399804007327 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 399804007328 substrate binding site [chemical binding]; other site 399804007329 active site 399804007330 catalytic residues [active] 399804007331 heterodimer interface [polypeptide binding]; other site 399804007332 ABC-type uncharacterized transport system involved in gliding motility, auxiliary component [Cell motility and secretion]; Region: GldG; COG3225 399804007333 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 399804007334 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 399804007335 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 399804007336 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 399804007337 Siderophore biosynthesis protein domain; Region: AlcB; smart01006 399804007338 Siderophore synthetase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: RhbC; COG4264 399804007339 IucA / IucC family; Region: IucA_IucC; pfam04183 399804007340 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 399804007341 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 399804007342 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 399804007343 N-terminal plug; other site 399804007344 ligand-binding site [chemical binding]; other site 399804007345 siderophore-iron reductase FhuF; Region: Fe_III_red_FhuF; TIGR03951 399804007346 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 399804007347 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 399804007348 intracellular septation protein A; Reviewed; Region: PRK00259 399804007349 YciI-like protein; Reviewed; Region: PRK11370 399804007350 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 399804007351 putative catalytic site [active] 399804007352 putative phosphate binding site [ion binding]; other site 399804007353 active site 399804007354 metal binding site A [ion binding]; metal-binding site 399804007355 DNA binding site [nucleotide binding] 399804007356 putative AP binding site [nucleotide binding]; other site 399804007357 putative metal binding site B [ion binding]; other site 399804007358 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804007359 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804007360 dimer interface [polypeptide binding]; other site 399804007361 putative CheW interface [polypeptide binding]; other site 399804007362 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 399804007363 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 399804007364 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 399804007365 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 399804007366 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 399804007367 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 399804007368 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 399804007369 catalytic loop [active] 399804007370 iron binding site [ion binding]; other site 399804007371 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 399804007372 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 399804007373 Ligand binding site; other site 399804007374 metal-binding site 399804007375 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 399804007376 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 399804007377 XdhC Rossmann domain; Region: XdhC_C; pfam13478 399804007378 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 399804007379 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 399804007380 DNA topoisomerase III; Provisional; Region: PRK07726 399804007381 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 399804007382 active site 399804007383 putative interdomain interaction site [polypeptide binding]; other site 399804007384 putative metal-binding site [ion binding]; other site 399804007385 putative nucleotide binding site [chemical binding]; other site 399804007386 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 399804007387 domain I; other site 399804007388 DNA binding groove [nucleotide binding] 399804007389 phosphate binding site [ion binding]; other site 399804007390 domain II; other site 399804007391 domain III; other site 399804007392 nucleotide binding site [chemical binding]; other site 399804007393 catalytic site [active] 399804007394 domain IV; other site 399804007395 amidophosphoribosyltransferase; Provisional; Region: PRK09246 399804007396 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 399804007397 active site 399804007398 tetramer interface [polypeptide binding]; other site 399804007399 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 399804007400 active site 399804007401 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 399804007402 Colicin V production protein; Region: Colicin_V; cl00567 399804007403 cell division protein DedD; Provisional; Region: PRK11633 399804007404 Sporulation related domain; Region: SPOR; pfam05036 399804007405 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 399804007406 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 399804007407 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 399804007408 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 399804007409 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 399804007410 dimerization interface 3.5A [polypeptide binding]; other site 399804007411 active site 399804007412 FimV N-terminal domain; Region: FimV_core; TIGR03505 399804007413 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 399804007414 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 399804007415 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 399804007416 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 399804007417 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 399804007418 ligand binding site [chemical binding]; other site 399804007419 NAD binding site [chemical binding]; other site 399804007420 catalytic site [active] 399804007421 homodimer interface [polypeptide binding]; other site 399804007422 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 399804007423 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 399804007424 dimer interface [polypeptide binding]; other site 399804007425 active site 399804007426 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 399804007427 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 399804007428 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 399804007429 YfcL protein; Region: YfcL; pfam08891 399804007430 Predicted inorganic polyphosphate/ATP-NAD kinase [General function prediction only]; Region: COG3199 399804007431 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 399804007432 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 399804007433 putative substrate translocation pore; other site 399804007434 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 399804007435 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 399804007436 Tetramer interface [polypeptide binding]; other site 399804007437 active site 399804007438 FMN-binding site [chemical binding]; other site 399804007439 HemK family putative methylases; Region: hemK_fam; TIGR00536 399804007440 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 399804007441 S-adenosylmethionine binding site [chemical binding]; other site 399804007442 hypothetical protein; Provisional; Region: PRK04946 399804007443 Smr domain; Region: Smr; pfam01713 399804007444 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 399804007445 catalytic core [active] 399804007446 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 399804007447 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 399804007448 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 399804007449 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 399804007450 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 399804007451 Two component regulator propeller; Region: Reg_prop; pfam07494 399804007452 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 399804007453 PAS fold; Region: PAS_3; pfam08447 399804007454 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 399804007455 PAS domain; Region: PAS_9; pfam13426 399804007456 putative active site [active] 399804007457 heme pocket [chemical binding]; other site 399804007458 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804007459 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804007460 metal binding site [ion binding]; metal-binding site 399804007461 active site 399804007462 I-site; other site 399804007463 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 399804007464 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 399804007465 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 399804007466 substrate binding site [chemical binding]; other site 399804007467 oxyanion hole (OAH) forming residues; other site 399804007468 trimer interface [polypeptide binding]; other site 399804007469 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 399804007470 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 399804007471 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 399804007472 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 399804007473 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 399804007474 dimer interface [polypeptide binding]; other site 399804007475 active site 399804007476 MoxR-like ATPases [General function prediction only]; Region: COG0714 399804007477 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 399804007478 Walker A motif; other site 399804007479 ATP binding site [chemical binding]; other site 399804007480 Walker B motif; other site 399804007481 arginine finger; other site 399804007482 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 399804007483 Protein of unknown function DUF58; Region: DUF58; pfam01882 399804007484 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 399804007485 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 399804007486 VWA BatA 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_BatA_type; cd01467 399804007487 metal ion-dependent adhesion site (MIDAS); other site 399804007488 von Willebrand factor type A domain; Region: VWA_2; pfam13519 399804007489 metal ion-dependent adhesion site (MIDAS); other site 399804007490 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 399804007491 binding surface 399804007492 TPR motif; other site 399804007493 Tetratricopeptide repeat; Region: TPR_16; pfam13432 399804007494 Oxygen tolerance; Region: BatD; pfam13584 399804007495 RNA polymerase sigma factor; Provisional; Region: PRK12517 399804007496 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 399804007497 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 399804007498 DNA binding residues [nucleotide binding] 399804007499 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 399804007500 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 399804007501 Na binding site [ion binding]; other site 399804007502 Glyoxalase-like domain; Region: Glyoxalase_2; pfam12681 399804007503 active site 399804007504 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 399804007505 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804007506 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804007507 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 399804007508 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 399804007509 active site residue [active] 399804007510 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 399804007511 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 399804007512 active site 399804007513 catalytic residues [active] 399804007514 PA_VapT_like: Protease-associated domain containing proteins like VapT from Vibrio metschnikovii strain RH530. This group contains various PA domain-containing proteins similar to V. metschnikovii VapT, including the serine alkaline protease SapSh from...; Region: PA_VapT_like; cd04817 399804007515 PA/subtilisin-like domain interface [polypeptide binding]; other site 399804007516 Subtilase family; Region: Peptidase_S8; pfam00082 399804007517 catalytic residues [active] 399804007518 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 399804007519 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 399804007520 YaeQ protein; Region: YaeQ; pfam07152 399804007521 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 399804007522 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 399804007523 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 399804007524 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 399804007525 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 399804007526 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 399804007527 Protein export membrane protein; Region: SecD_SecF; pfam02355 399804007528 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 399804007529 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 399804007530 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 399804007531 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 399804007532 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 399804007533 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 399804007534 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 399804007535 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 399804007536 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 399804007537 Protein of unknown function, DUF479; Region: DUF479; pfam04336 399804007538 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 399804007539 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 399804007540 active site 399804007541 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 399804007542 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 399804007543 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; pfam08547 399804007544 serine/threonine transporter SstT; Provisional; Region: PRK13628 399804007545 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 399804007546 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 399804007547 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 399804007548 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 399804007549 active site 399804007550 phosphorylation site [posttranslational modification] 399804007551 intermolecular recognition site; other site 399804007552 dimerization interface [polypeptide binding]; other site 399804007553 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 399804007554 active site 399804007555 catalytic residues [active] 399804007556 helicase 45; Provisional; Region: PTZ00424 399804007557 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 399804007558 ATP binding site [chemical binding]; other site 399804007559 Mg++ binding site [ion binding]; other site 399804007560 motif III; other site 399804007561 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 399804007562 nucleotide binding region [chemical binding]; other site 399804007563 ATP-binding site [chemical binding]; other site 399804007564 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 399804007565 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 399804007566 DNA binding site [nucleotide binding] 399804007567 active site 399804007568 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 399804007569 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 399804007570 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804007571 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804007572 AlkA N-terminal domain; Region: AlkA_N; pfam06029 399804007573 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 399804007574 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 399804007575 minor groove reading motif; other site 399804007576 helix-hairpin-helix signature motif; other site 399804007577 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 399804007578 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804007579 ABC transporter signature motif; other site 399804007580 Walker B; other site 399804007581 D-loop; other site 399804007582 H-loop/switch region; other site 399804007583 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804007584 Walker A/P-loop; other site 399804007585 ATP binding site [chemical binding]; other site 399804007586 Q-loop/lid; other site 399804007587 ABC transporter signature motif; other site 399804007588 Walker B; other site 399804007589 D-loop; other site 399804007590 H-loop/switch region; other site 399804007591 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 399804007592 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 399804007593 FeS/SAM binding site; other site 399804007594 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 399804007595 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 399804007596 active site 399804007597 iron coordination sites [ion binding]; other site 399804007598 Uncharacterized conserved protein [Function unknown]; Region: COG4278 399804007599 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 399804007600 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 399804007601 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 399804007602 Walker A/P-loop; other site 399804007603 ATP binding site [chemical binding]; other site 399804007604 Q-loop/lid; other site 399804007605 ABC transporter signature motif; other site 399804007606 Walker B; other site 399804007607 D-loop; other site 399804007608 H-loop/switch region; other site 399804007609 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 399804007610 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 399804007611 active site 399804007612 HIGH motif; other site 399804007613 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 399804007614 active site 399804007615 KMSKS motif; other site 399804007616 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 399804007617 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 399804007618 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 399804007619 DctM-like transporters; Region: DctM; pfam06808 399804007620 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 399804007621 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 399804007622 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 399804007623 dimer interface [polypeptide binding]; other site 399804007624 phosphorylation site [posttranslational modification] 399804007625 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 399804007626 ATP binding site [chemical binding]; other site 399804007627 Mg2+ binding site [ion binding]; other site 399804007628 G-X-G motif; other site 399804007629 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 399804007630 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 399804007631 active site 399804007632 phosphorylation site [posttranslational modification] 399804007633 intermolecular recognition site; other site 399804007634 dimerization interface [polypeptide binding]; other site 399804007635 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 399804007636 Walker A motif; other site 399804007637 ATP binding site [chemical binding]; other site 399804007638 Walker B motif; other site 399804007639 arginine finger; other site 399804007640 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804007641 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 399804007642 Transglycosylase; Region: Transgly; cl17702 399804007643 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 399804007644 thymidine kinase; Provisional; Region: PRK04296 399804007645 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 399804007646 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 399804007647 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 399804007648 active site 399804007649 Zn binding site [ion binding]; other site 399804007650 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 399804007651 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 399804007652 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 399804007653 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 399804007654 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 399804007655 Ligand binding site [chemical binding]; other site 399804007656 Electron transfer flavoprotein domain; Region: ETF; pfam01012 399804007657 Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA; Region: Topoisomer_IB_N; cl02774 399804007658 H-NS histone family; Region: Histone_HNS; pfam00816 399804007659 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 399804007660 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804007661 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804007662 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 399804007663 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 399804007664 active site 399804007665 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 399804007666 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 399804007667 homodimer interaction site [polypeptide binding]; other site 399804007668 cofactor binding site; other site 399804007669 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 399804007670 putative CoA binding site [chemical binding]; other site 399804007671 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 399804007672 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 399804007673 trimer interface [polypeptide binding]; other site 399804007674 active site 399804007675 substrate binding site [chemical binding]; other site 399804007676 CoA binding site [chemical binding]; other site 399804007677 prolyl-tRNA synthetase; Provisional; Region: PRK09194 399804007678 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 399804007679 dimer interface [polypeptide binding]; other site 399804007680 motif 1; other site 399804007681 active site 399804007682 motif 2; other site 399804007683 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 399804007684 putative deacylase active site [active] 399804007685 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 399804007686 active site 399804007687 motif 3; other site 399804007688 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 399804007689 anticodon binding site; other site 399804007690 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 399804007691 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 399804007692 nucleophile elbow; other site 399804007693 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 399804007694 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 399804007695 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 399804007696 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 399804007697 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 399804007698 active site 399804007699 FMN binding site [chemical binding]; other site 399804007700 substrate binding site [chemical binding]; other site 399804007701 homotetramer interface [polypeptide binding]; other site 399804007702 catalytic residue [active] 399804007703 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 399804007704 Transposase; Region: HTH_Tnp_1; pfam01527 399804007705 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 399804007706 putative transposase OrfB; Reviewed; Region: PHA02517 399804007707 HTH-like domain; Region: HTH_21; pfam13276 399804007708 Integrase core domain; Region: rve; pfam00665 399804007709 Integrase core domain; Region: rve_2; pfam13333 399804007710 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804007711 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 399804007712 putative active site [active] 399804007713 putative metal binding site [ion binding]; other site 399804007714 Cytochrome c552; Region: Cytochrom_C552; pfam02335 399804007715 NnrS protein; Region: NnrS; pfam05940 399804007716 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 399804007717 Protein of unknown function (DUF1778); Region: DUF1778; pfam08681 399804007718 Transposase; Region: HTH_Tnp_1; pfam01527 399804007719 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 399804007720 putative transposase OrfB; Reviewed; Region: PHA02517 399804007721 HTH-like domain; Region: HTH_21; pfam13276 399804007722 Integrase core domain; Region: rve; pfam00665 399804007723 Integrase core domain; Region: rve_2; pfam13333 399804007724 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804007725 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 399804007726 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 399804007727 NAD binding site [chemical binding]; other site 399804007728 substrate binding site [chemical binding]; other site 399804007729 homodimer interface [polypeptide binding]; other site 399804007730 active site 399804007731 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 399804007732 Transposase; Region: DDE_Tnp_ISL3; pfam01610 399804007733 lipoprotein signal peptidase; Provisional; Region: PRK14776 399804007734 Heavy-metal-associated domain; Region: HMA; pfam00403 399804007735 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 399804007736 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 399804007737 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 399804007738 DNA binding residues [nucleotide binding] 399804007739 dimer interface [polypeptide binding]; other site 399804007740 putative metal binding site [ion binding]; other site 399804007741 mobile mystery protein B; Region: mob_myst_B; TIGR02613 399804007742 Fic/DOC family; Region: Fic; pfam02661 399804007743 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 399804007744 HicB family; Region: HicB; pfam05534 399804007745 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 399804007746 non-specific DNA binding site [nucleotide binding]; other site 399804007747 salt bridge; other site 399804007748 sequence-specific DNA binding site [nucleotide binding]; other site 399804007749 HipA N-terminal domain; Region: Couple_hipA; cl11853 399804007750 HipA-like N-terminal domain; Region: HipA_N; pfam07805 399804007751 HipA-like C-terminal domain; Region: HipA_C; pfam07804 399804007752 CcdB protein; Region: CcdB; pfam01845 399804007753 Post-segregation antitoxin CcdA; Region: CcdA; pfam07362 399804007754 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 399804007755 Integrase core domain; Region: rve; pfam00665 399804007756 transposase/IS protein; Provisional; Region: PRK09183 399804007757 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 399804007758 Walker A motif; other site 399804007759 ATP binding site [chemical binding]; other site 399804007760 Walker B motif; other site 399804007761 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 399804007762 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 399804007763 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 399804007764 active site 399804007765 DNA binding site [nucleotide binding] 399804007766 Int/Topo IB signature motif; other site 399804007767 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 399804007768 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 399804007769 HicB family; Region: HicB; pfam05534 399804007770 PemK-like protein; Region: PemK; cl00995 399804007771 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 399804007772 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 399804007773 putative addiction module antidote protein, CC2985 family; Region: antidote_CC2985; TIGR02606 399804007774 HipA N-terminal domain; Region: Couple_hipA; cl11853 399804007775 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 399804007776 non-specific DNA binding site [nucleotide binding]; other site 399804007777 salt bridge; other site 399804007778 sequence-specific DNA binding site [nucleotide binding]; other site 399804007779 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 399804007780 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 399804007781 Probable transposase; Region: OrfB_IS605; pfam01385 399804007782 Transposase IS200 like; Region: Y1_Tnp; pfam01797 399804007783 potassium/proton antiporter; Reviewed; Region: PRK05326 399804007784 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 399804007785 TrkA-C domain; Region: TrkA_C; pfam02080 399804007786 Transporter associated domain; Region: CorC_HlyC; smart01091 399804007787 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 399804007788 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804007789 bifunctional antitoxin/transcriptional repressor RelB; Provisional; Region: PRK11235 399804007790 Homeodomain-like domain; Region: HTH_23; pfam13384 399804007791 Winged helix-turn helix; Region: HTH_29; pfam13551 399804007792 Winged helix-turn helix; Region: HTH_33; pfam13592 399804007793 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804007794 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804007795 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 399804007796 Uncharacterized protein family (UPF0156); Region: RHH_2; pfam03693 399804007797 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 399804007798 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 399804007799 Probable transposase; Region: OrfB_IS605; pfam01385 399804007800 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804007801 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 399804007802 putative addiction module antidote protein, CC2985 family; Region: antidote_CC2985; TIGR02606 399804007803 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 399804007804 Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient...; Region: SR_Res_par; cd03767 399804007805 catalytic residues [active] 399804007806 catalytic nucleophile [active] 399804007807 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 399804007808 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 399804007809 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 399804007810 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 399804007811 active site 399804007812 DNA binding site [nucleotide binding] 399804007813 Int/Topo IB signature motif; other site 399804007814 Zeta toxin; Region: Zeta_toxin; pfam06414 399804007815 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 399804007816 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 399804007817 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 399804007818 NAD binding site [chemical binding]; other site 399804007819 substrate binding site [chemical binding]; other site 399804007820 homodimer interface [polypeptide binding]; other site 399804007821 active site 399804007822 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 399804007823 non-specific DNA binding site [nucleotide binding]; other site 399804007824 salt bridge; other site 399804007825 sequence-specific DNA binding site [nucleotide binding]; other site 399804007826 mobile mystery protein B; Region: mob_myst_B; TIGR02613 399804007827 Fic/DOC family; Region: Fic; pfam02661 399804007828 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 399804007829 HicB family; Region: HicB; pfam05534 399804007830 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 399804007831 non-specific DNA binding site [nucleotide binding]; other site 399804007832 salt bridge; other site 399804007833 sequence-specific DNA binding site [nucleotide binding]; other site 399804007834 HipA N-terminal domain; Region: Couple_hipA; cl11853 399804007835 HipA-like N-terminal domain; Region: HipA_N; pfam07805 399804007836 HipA-like C-terminal domain; Region: HipA_C; pfam07804 399804007837 CcdB protein; Region: CcdB; pfam01845 399804007838 Post-segregation antitoxin CcdA; Region: CcdA; pfam07362 399804007839 HipA N-terminal domain; Region: Couple_hipA; cl11853 399804007840 HipA-like N-terminal domain; Region: HipA_N; pfam07805 399804007841 HipA-like C-terminal domain; Region: HipA_C; pfam07804 399804007842 PemK-like protein; Region: PemK; cl00995 399804007843 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 399804007844 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 399804007845 putative addiction module antidote protein, CC2985 family; Region: antidote_CC2985; TIGR02606 399804007846 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 399804007847 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; pfam09907 399804007848 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 399804007849 Predicted transcriptional regulator [Transcription]; Region: COG3905 399804007850 primosomal protein DnaI; Provisional; Region: PRK02854 399804007851 Toxin YafO, type II toxin-antitoxin system; Region: YafO_toxin; cl08066 399804007852 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 399804007853 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 399804007854 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 399804007855 active site 399804007856 substrate binding site [chemical binding]; other site 399804007857 metal binding site [ion binding]; metal-binding site 399804007858 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 399804007859 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 399804007860 Mg++ binding site [ion binding]; other site 399804007861 putative catalytic motif [active] 399804007862 substrate binding site [chemical binding]; other site 399804007863 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 399804007864 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 399804007865 Mg++ binding site [ion binding]; other site 399804007866 putative catalytic motif [active] 399804007867 substrate binding site [chemical binding]; other site 399804007868 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 399804007869 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 399804007870 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 399804007871 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 399804007872 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 399804007873 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 399804007874 putative NAD(P) binding site [chemical binding]; other site 399804007875 active site 399804007876 putative substrate binding site [chemical binding]; other site 399804007877 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804007878 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 399804007879 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 399804007880 O-Antigen ligase; Region: Wzy_C; pfam04932 399804007881 TupA-like ATPgrasp; Region: ATPgrasp_TupA; pfam14305 399804007882 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 399804007883 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 399804007884 putative active site [active] 399804007885 putative metal binding site [ion binding]; other site 399804007886 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 399804007887 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 399804007888 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 399804007889 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 399804007890 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 399804007891 hinge; other site 399804007892 active site 399804007893 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 399804007894 FAD binding domain; Region: FAD_binding_4; pfam01565 399804007895 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 399804007896 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 399804007897 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 399804007898 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 399804007899 NADP binding site [chemical binding]; other site 399804007900 active site 399804007901 putative substrate binding site [chemical binding]; other site 399804007902 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 399804007903 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 399804007904 substrate binding site; other site 399804007905 tetramer interface; other site 399804007906 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 399804007907 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 399804007908 NAD binding site [chemical binding]; other site 399804007909 substrate binding site [chemical binding]; other site 399804007910 homodimer interface [polypeptide binding]; other site 399804007911 active site 399804007912 Chain length determinant protein; Region: Wzz; pfam02706 399804007913 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 399804007914 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 399804007915 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 399804007916 SLBB domain; Region: SLBB; pfam10531 399804007917 SLBB domain; Region: SLBB; pfam10531 399804007918 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 399804007919 SLBB domain; Region: SLBB; pfam10531 399804007920 SLBB domain; Region: SLBB; pfam10531 399804007921 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 399804007922 transcriptional activator RfaH; Region: RfaH; TIGR01955 399804007923 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 399804007924 heterodimer interface [polypeptide binding]; other site 399804007925 homodimer interface [polypeptide binding]; other site 399804007926 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 399804007927 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 399804007928 putative substrate translocation pore; other site 399804007929 Response regulator receiver domain; Region: Response_reg; pfam00072 399804007930 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 399804007931 active site 399804007932 phosphorylation site [posttranslational modification] 399804007933 intermolecular recognition site; other site 399804007934 dimerization interface [polypeptide binding]; other site 399804007935 VacJ like lipoprotein; Region: VacJ; cl01073 399804007936 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 399804007937 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 399804007938 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 399804007939 putative CheA interaction surface; other site 399804007940 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 399804007941 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 399804007942 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 399804007943 P-loop; other site 399804007944 Magnesium ion binding site [ion binding]; other site 399804007945 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 399804007946 Magnesium ion binding site [ion binding]; other site 399804007947 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 399804007948 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 399804007949 active site 399804007950 phosphorylation site [posttranslational modification] 399804007951 intermolecular recognition site; other site 399804007952 CheB methylesterase; Region: CheB_methylest; pfam01339 399804007953 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 399804007954 putative binding surface; other site 399804007955 active site 399804007956 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 399804007957 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 399804007958 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 399804007959 ATP binding site [chemical binding]; other site 399804007960 Mg2+ binding site [ion binding]; other site 399804007961 G-X-G motif; other site 399804007962 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 399804007963 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 399804007964 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 399804007965 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 399804007966 active site 399804007967 phosphorylation site [posttranslational modification] 399804007968 intermolecular recognition site; other site 399804007969 dimerization interface [polypeptide binding]; other site 399804007970 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 399804007971 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 399804007972 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 399804007973 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 399804007974 DNA binding residues [nucleotide binding] 399804007975 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 399804007976 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 399804007977 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 399804007978 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 399804007979 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 399804007980 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 399804007981 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 399804007982 FHIPEP family; Region: FHIPEP; pfam00771 399804007983 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 399804007984 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 399804007985 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 399804007986 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 399804007987 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 399804007988 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 399804007989 flagellar motor switch protein; Validated; Region: fliN; PRK08983 399804007990 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 399804007991 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 399804007992 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK05696 399804007993 Cornifin (SPRR) family; Region: Cornifin; pfam02389 399804007994 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 399804007995 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 399804007996 Flagellar FliJ protein; Region: FliJ; pfam02050 399804007997 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08972 399804007998 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 399804007999 Walker A motif/ATP binding site; other site 399804008000 Walker B motif; other site 399804008001 flagellar assembly protein H; Validated; Region: fliH; PRK05687 399804008002 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 399804008003 Flagellar assembly protein FliH; Region: FliH; pfam02108 399804008004 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 399804008005 MgtE intracellular N domain; Region: MgtE_N; smart00924 399804008006 FliG C-terminal domain; Region: FliG_C; pfam01706 399804008007 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 399804008008 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 399804008009 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 399804008010 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 399804008011 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 399804008012 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 399804008013 active site 399804008014 phosphorylation site [posttranslational modification] 399804008015 intermolecular recognition site; other site 399804008016 dimerization interface [polypeptide binding]; other site 399804008017 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 399804008018 Walker A motif; other site 399804008019 ATP binding site [chemical binding]; other site 399804008020 Walker B motif; other site 399804008021 arginine finger; other site 399804008022 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804008023 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 399804008024 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 399804008025 putative active site [active] 399804008026 heme pocket [chemical binding]; other site 399804008027 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 399804008028 dimer interface [polypeptide binding]; other site 399804008029 phosphorylation site [posttranslational modification] 399804008030 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 399804008031 ATP binding site [chemical binding]; other site 399804008032 Mg2+ binding site [ion binding]; other site 399804008033 G-X-G motif; other site 399804008034 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 399804008035 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 399804008036 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 399804008037 Walker A motif; other site 399804008038 ATP binding site [chemical binding]; other site 399804008039 Walker B motif; other site 399804008040 arginine finger; other site 399804008041 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804008042 flagellar protein FliS; Validated; Region: fliS; PRK05685 399804008043 flagellar capping protein; Reviewed; Region: fliD; PRK08032 399804008044 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 399804008045 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 399804008046 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 399804008047 FlaG protein; Region: FlaG; pfam03646 399804008048 flagellin; Provisional; Region: PRK12802 399804008049 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 399804008050 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 399804008051 flagellin; Provisional; Region: PRK12802 399804008052 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 399804008053 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 399804008054 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 399804008055 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 399804008056 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08871 399804008057 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 399804008058 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 399804008059 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 399804008060 flagellar rod assembly protein/muramidase FlgJ; Region: flagell_FlgJ; TIGR02541 399804008061 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 399804008062 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 399804008063 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 399804008064 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 399804008065 Flagellar L-ring protein; Region: FlgH; pfam02107 399804008066 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 399804008067 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 399804008068 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 399804008069 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 399804008070 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 399804008071 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 399804008072 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 399804008073 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 399804008074 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 399804008075 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 399804008076 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 399804008077 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12631 399804008078 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 399804008079 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 399804008080 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12625 399804008081 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 399804008082 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 399804008083 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 399804008084 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 399804008085 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 399804008086 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 399804008087 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 399804008088 active site 399804008089 phosphorylation site [posttranslational modification] 399804008090 intermolecular recognition site; other site 399804008091 dimerization interface [polypeptide binding]; other site 399804008092 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 399804008093 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 399804008094 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 399804008095 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 399804008096 FlgN protein; Region: FlgN; pfam05130 399804008097 LPP20 lipoprotein; Region: LPP20; pfam02169 399804008098 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804008099 Protein of unknown function (DUF2947); Region: DUF2947; pfam11163 399804008100 rhombotail lipoprotein; Region: rhombo_lipo; TIGR04179 399804008101 Protein of unknown function (DUF3308); Region: DUF3308; cl14675 399804008102 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804008103 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804008104 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804008105 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804008106 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804008107 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804008108 HAMP domain; Region: HAMP; pfam00672 399804008109 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804008110 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804008111 dimer interface [polypeptide binding]; other site 399804008112 putative CheW interface [polypeptide binding]; other site 399804008113 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 399804008114 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 399804008115 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 399804008116 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 399804008117 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 399804008118 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 399804008119 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 399804008120 dimerization interface [polypeptide binding]; other site 399804008121 ATP binding site [chemical binding]; other site 399804008122 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 399804008123 dimerization interface [polypeptide binding]; other site 399804008124 ATP binding site [chemical binding]; other site 399804008125 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 399804008126 putative active site [active] 399804008127 catalytic triad [active] 399804008128 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 399804008129 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 399804008130 substrate binding pocket [chemical binding]; other site 399804008131 membrane-bound complex binding site; other site 399804008132 hinge residues; other site 399804008133 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 399804008134 N-acetyl-D-glucosamine binding site [chemical binding]; other site 399804008135 catalytic residue [active] 399804008136 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 399804008137 nucleoside/Zn binding site; other site 399804008138 dimer interface [polypeptide binding]; other site 399804008139 catalytic motif [active] 399804008140 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804008141 GMP synthase; Reviewed; Region: guaA; PRK00074 399804008142 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 399804008143 AMP/PPi binding site [chemical binding]; other site 399804008144 candidate oxyanion hole; other site 399804008145 catalytic triad [active] 399804008146 potential glutamine specificity residues [chemical binding]; other site 399804008147 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 399804008148 ATP Binding subdomain [chemical binding]; other site 399804008149 Ligand Binding sites [chemical binding]; other site 399804008150 Dimerization subdomain; other site 399804008151 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 399804008152 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 399804008153 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 399804008154 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 399804008155 active site 399804008156 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 399804008157 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 399804008158 generic binding surface II; other site 399804008159 generic binding surface I; other site 399804008160 GTP-binding protein Der; Reviewed; Region: PRK00093 399804008161 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 399804008162 G1 box; other site 399804008163 GTP/Mg2+ binding site [chemical binding]; other site 399804008164 Switch I region; other site 399804008165 G2 box; other site 399804008166 Switch II region; other site 399804008167 G3 box; other site 399804008168 G4 box; other site 399804008169 G5 box; other site 399804008170 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 399804008171 G1 box; other site 399804008172 GTP/Mg2+ binding site [chemical binding]; other site 399804008173 Switch I region; other site 399804008174 G2 box; other site 399804008175 G3 box; other site 399804008176 Switch II region; other site 399804008177 G4 box; other site 399804008178 G5 box; other site 399804008179 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 399804008180 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 399804008181 active site 399804008182 Trp docking motif [polypeptide binding]; other site 399804008183 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 399804008184 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 399804008185 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 399804008186 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 399804008187 dimer interface [polypeptide binding]; other site 399804008188 motif 1; other site 399804008189 active site 399804008190 motif 2; other site 399804008191 motif 3; other site 399804008192 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 399804008193 anticodon binding site; other site 399804008194 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 399804008195 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 399804008196 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 399804008197 cytoskeletal protein RodZ; Provisional; Region: PRK10856 399804008198 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 399804008199 non-specific DNA binding site [nucleotide binding]; other site 399804008200 salt bridge; other site 399804008201 sequence-specific DNA binding site [nucleotide binding]; other site 399804008202 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 399804008203 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 399804008204 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 399804008205 binding surface 399804008206 TPR motif; other site 399804008207 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 399804008208 TPR motif; other site 399804008209 binding surface 399804008210 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 399804008211 binding surface 399804008212 TPR motif; other site 399804008213 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 399804008214 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 399804008215 FeS/SAM binding site; other site 399804008216 Domain of unknown function DUF21; Region: DUF21; pfam01595 399804008217 FOG: CBS domain [General function prediction only]; Region: COG0517 399804008218 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 399804008219 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 399804008220 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 399804008221 active site 399804008222 metal binding site [ion binding]; metal-binding site 399804008223 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 399804008224 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804008225 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 399804008226 The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; Region: PBP2_HupR; cd08431 399804008227 putative dimerization interface [polypeptide binding]; other site 399804008228 Predicted membrane protein [Function unknown]; Region: COG2259 399804008229 Pirin-related protein [General function prediction only]; Region: COG1741 399804008230 Pirin; Region: Pirin; pfam02678 399804008231 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 399804008232 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804008233 Coenzyme A binding pocket [chemical binding]; other site 399804008234 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 399804008235 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804008236 Coenzyme A binding pocket [chemical binding]; other site 399804008237 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 399804008238 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 399804008239 Coenzyme A binding pocket [chemical binding]; other site 399804008240 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 399804008241 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 399804008242 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804008243 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804008244 metal binding site [ion binding]; metal-binding site 399804008245 active site 399804008246 I-site; other site 399804008247 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 399804008248 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 399804008249 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 399804008250 tetramer interface [polypeptide binding]; other site 399804008251 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804008252 catalytic residue [active] 399804008253 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 399804008254 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804008255 ligand binding site [chemical binding]; other site 399804008256 mechanosensitive channel MscS; Provisional; Region: PRK10334 399804008257 Conserved TM helix; Region: TM_helix; pfam05552 399804008258 Mechanosensitive ion channel; Region: MS_channel; pfam00924 399804008259 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 399804008260 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 399804008261 dimer interface [polypeptide binding]; other site 399804008262 catalytic triad [active] 399804008263 peroxidatic and resolving cysteines [active] 399804008264 Predicted membrane protein [Function unknown]; Region: COG2860 399804008265 UPF0126 domain; Region: UPF0126; pfam03458 399804008266 UPF0126 domain; Region: UPF0126; pfam03458 399804008267 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 399804008268 translation initiation factor Sui1; Validated; Region: PRK06824 399804008269 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 399804008270 putative rRNA binding site [nucleotide binding]; other site 399804008271 hypothetical protein; Validated; Region: PRK00228 399804008272 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 399804008273 ferrochelatase; Reviewed; Region: hemH; PRK00035 399804008274 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 399804008275 active site 399804008276 C-terminal domain interface [polypeptide binding]; other site 399804008277 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 399804008278 active site 399804008279 N-terminal domain interface [polypeptide binding]; other site 399804008280 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 399804008281 catalytic residues [active] 399804008282 dimer interface [polypeptide binding]; other site 399804008283 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 399804008284 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 399804008285 Walker A motif; other site 399804008286 ATP binding site [chemical binding]; other site 399804008287 Walker B motif; other site 399804008288 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 399804008289 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 399804008290 Walker A motif; other site 399804008291 ATP binding site [chemical binding]; other site 399804008292 Walker B motif; other site 399804008293 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 399804008294 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 399804008295 catalytic residue [active] 399804008296 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 399804008297 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 399804008298 YGGT family; Region: YGGT; pfam02325 399804008299 YGGT family; Region: YGGT; pfam02325 399804008300 hypothetical protein; Validated; Region: PRK05090 399804008301 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 399804008302 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 399804008303 active site 399804008304 dimerization interface [polypeptide binding]; other site 399804008305 HemN family oxidoreductase; Provisional; Region: PRK05660 399804008306 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 399804008307 FeS/SAM binding site; other site 399804008308 HemN C-terminal domain; Region: HemN_C; pfam06969 399804008309 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 399804008310 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804008311 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804008312 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 399804008313 putative effector binding pocket; other site 399804008314 dimerization interface [polypeptide binding]; other site 399804008315 Protein of unknown function (DUF2884); Region: DUF2884; pfam11101 399804008316 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 399804008317 glutaminase; Provisional; Region: PRK00971 399804008318 hypothetical protein; Provisional; Region: PRK11702 399804008319 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 399804008320 S-adenosylmethionine binding site [chemical binding]; other site 399804008321 adenine DNA glycosylase; Provisional; Region: PRK10880 399804008322 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 399804008323 minor groove reading motif; other site 399804008324 helix-hairpin-helix signature motif; other site 399804008325 substrate binding pocket [chemical binding]; other site 399804008326 active site 399804008327 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 399804008328 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 399804008329 DNA binding and oxoG recognition site [nucleotide binding] 399804008330 oxidative damage protection protein; Provisional; Region: PRK05408 399804008331 hypothetical protein; Provisional; Region: PRK03757 399804008332 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 399804008333 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 399804008334 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 399804008335 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 399804008336 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 399804008337 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 399804008338 S-adenosylmethionine binding site [chemical binding]; other site 399804008339 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 399804008340 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 399804008341 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 399804008342 short chain dehydrogenase; Provisional; Region: PRK06123 399804008343 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804008344 NAD(P) binding site [chemical binding]; other site 399804008345 active site 399804008346 SnoaL-like domain; Region: SnoaL_2; pfam12680 399804008347 DNA photolyase; Region: DNA_photolyase; pfam00875 399804008348 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 399804008349 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 399804008350 DNA binding residues [nucleotide binding] 399804008351 Protein of unknown function (DUF523); Region: DUF523; pfam04463 399804008352 Uncharacterized conserved protein [Function unknown]; Region: COG3272 399804008353 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 399804008354 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 399804008355 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 399804008356 DEAD-like helicases superfamily; Region: DEXDc; smart00487 399804008357 ATP binding site [chemical binding]; other site 399804008358 Mg++ binding site [ion binding]; other site 399804008359 motif III; other site 399804008360 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 399804008361 nucleotide binding region [chemical binding]; other site 399804008362 ATP-binding site [chemical binding]; other site 399804008363 AAA domain; Region: AAA_32; pfam13654 399804008364 lon-related putative ATP-dependent protease; Region: lon_rel; TIGR00764 399804008365 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 399804008366 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 399804008367 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 399804008368 FMN binding site [chemical binding]; other site 399804008369 active site 399804008370 substrate binding site [chemical binding]; other site 399804008371 catalytic residue [active] 399804008372 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804008373 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804008374 Protein of unknown function (DUF2375); Region: DUF2375; pfam09558 399804008375 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804008376 dimer interface [polypeptide binding]; other site 399804008377 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 399804008378 putative CheW interface [polypeptide binding]; other site 399804008379 hypothetical protein; Provisional; Region: PRK12378 399804008380 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 399804008381 30S subunit binding site; other site 399804008382 PAS domain; Region: PAS_9; pfam13426 399804008383 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 399804008384 putative active site [active] 399804008385 heme pocket [chemical binding]; other site 399804008386 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804008387 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804008388 dimer interface [polypeptide binding]; other site 399804008389 putative CheW interface [polypeptide binding]; other site 399804008390 Protein of unknown function (DUF3649); Region: DUF3649; pfam12365 399804008391 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 399804008392 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 399804008393 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 399804008394 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 399804008395 OsmC-like protein; Region: OsmC; cl00767 399804008396 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 399804008397 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804008398 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 399804008399 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 399804008400 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 399804008401 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 399804008402 protein binding site [polypeptide binding]; other site 399804008403 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 399804008404 Domain interface; other site 399804008405 Peptide binding site; other site 399804008406 Active site tetrad [active] 399804008407 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 399804008408 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804008409 substrate binding pocket [chemical binding]; other site 399804008410 membrane-bound complex binding site; other site 399804008411 hinge residues; other site 399804008412 threonine synthase; Validated; Region: PRK09225 399804008413 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 399804008414 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 399804008415 catalytic residue [active] 399804008416 homoserine kinase; Provisional; Region: PRK01212 399804008417 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 399804008418 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 399804008419 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 399804008420 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 399804008421 putative catalytic residues [active] 399804008422 putative nucleotide binding site [chemical binding]; other site 399804008423 putative aspartate binding site [chemical binding]; other site 399804008424 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 399804008425 dimer interface [polypeptide binding]; other site 399804008426 putative threonine allosteric regulatory site; other site 399804008427 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 399804008428 putative threonine allosteric regulatory site; other site 399804008429 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 399804008430 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 399804008431 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 399804008432 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804008433 Trp repressor protein; Region: Trp_repressor; pfam01371 399804008434 Cytochrome C' Region: Cytochrom_C_2; pfam01322 399804008435 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 399804008436 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 399804008437 30S subunit binding site; other site 399804008438 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 399804008439 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 399804008440 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 399804008441 HIGH motif; other site 399804008442 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 399804008443 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 399804008444 active site 399804008445 KMSKS motif; other site 399804008446 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 399804008447 tRNA binding surface [nucleotide binding]; other site 399804008448 anticodon binding site; other site 399804008449 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 399804008450 carbon storage regulator; Provisional; Region: PRK01712 399804008451 aspartate kinase; Reviewed; Region: PRK06635 399804008452 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 399804008453 putative nucleotide binding site [chemical binding]; other site 399804008454 putative catalytic residues [active] 399804008455 putative Mg ion binding site [ion binding]; other site 399804008456 putative aspartate binding site [chemical binding]; other site 399804008457 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 399804008458 putative allosteric regulatory residue; other site 399804008459 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 399804008460 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 399804008461 motif 1; other site 399804008462 active site 399804008463 motif 2; other site 399804008464 motif 3; other site 399804008465 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 399804008466 DHHA1 domain; Region: DHHA1; pfam02272 399804008467 RecX family; Region: RecX; pfam02631 399804008468 recombinase A; Provisional; Region: recA; PRK09354 399804008469 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 399804008470 hexamer interface [polypeptide binding]; other site 399804008471 Walker A motif; other site 399804008472 ATP binding site [chemical binding]; other site 399804008473 Walker B motif; other site 399804008474 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 399804008475 MutS domain I; Region: MutS_I; pfam01624 399804008476 MutS domain II; Region: MutS_II; pfam05188 399804008477 MutS domain III; Region: MutS_III; pfam05192 399804008478 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 399804008479 Walker A/P-loop; other site 399804008480 ATP binding site [chemical binding]; other site 399804008481 Q-loop/lid; other site 399804008482 ABC transporter signature motif; other site 399804008483 Walker B; other site 399804008484 D-loop; other site 399804008485 H-loop/switch region; other site 399804008486 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 399804008487 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804008488 Peptidase family M23; Region: Peptidase_M23; pfam01551 399804008489 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 399804008490 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 399804008491 S-adenosylmethionine binding site [chemical binding]; other site 399804008492 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 399804008493 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 399804008494 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 399804008495 Permutation of conserved domain; other site 399804008496 active site 399804008497 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 399804008498 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 399804008499 homotrimer interaction site [polypeptide binding]; other site 399804008500 zinc binding site [ion binding]; other site 399804008501 CDP-binding sites; other site 399804008502 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 399804008503 substrate binding site; other site 399804008504 dimer interface; other site 399804008505 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 399804008506 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 399804008507 enolase; Provisional; Region: eno; PRK00077 399804008508 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 399804008509 dimer interface [polypeptide binding]; other site 399804008510 metal binding site [ion binding]; metal-binding site 399804008511 substrate binding pocket [chemical binding]; other site 399804008512 CTP synthetase; Validated; Region: pyrG; PRK05380 399804008513 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 399804008514 Catalytic site [active] 399804008515 active site 399804008516 UTP binding site [chemical binding]; other site 399804008517 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 399804008518 active site 399804008519 putative oxyanion hole; other site 399804008520 catalytic triad [active] 399804008521 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 399804008522 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 399804008523 homodimer interface [polypeptide binding]; other site 399804008524 metal binding site [ion binding]; metal-binding site 399804008525 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 399804008526 homodimer interface [polypeptide binding]; other site 399804008527 active site 399804008528 putative chemical substrate binding site [chemical binding]; other site 399804008529 metal binding site [ion binding]; metal-binding site 399804008530 agmatine deiminase; Provisional; Region: PRK13551 399804008531 agmatine deiminase; Region: agmatine_aguA; TIGR03380 399804008532 amidase; Validated; Region: PRK06565 399804008533 Amidase; Region: Amidase; cl11426 399804008534 Amidase; Region: Amidase; cl11426 399804008535 methionine synthase; Provisional; Region: PRK01207 399804008536 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 399804008537 substrate binding site [chemical binding]; other site 399804008538 THF binding site; other site 399804008539 zinc-binding site [ion binding]; other site 399804008540 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 399804008541 AAA domain; Region: AAA_11; pfam13086 399804008542 Part of AAA domain; Region: AAA_19; pfam13245 399804008543 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 399804008544 AAA domain; Region: AAA_12; pfam13087 399804008545 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 399804008546 putative active site [active] 399804008547 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 399804008548 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 399804008549 HD domain; Region: HD_4; pfam13328 399804008550 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 399804008551 synthetase active site [active] 399804008552 NTP binding site [chemical binding]; other site 399804008553 metal binding site [ion binding]; metal-binding site 399804008554 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 399804008555 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 399804008556 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 399804008557 TRAM domain; Region: TRAM; pfam01938 399804008558 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 399804008559 S-adenosylmethionine binding site [chemical binding]; other site 399804008560 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 399804008561 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 399804008562 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 399804008563 dimerization interface [polypeptide binding]; other site 399804008564 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 399804008565 dimer interface [polypeptide binding]; other site 399804008566 phosphorylation site [posttranslational modification] 399804008567 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 399804008568 ATP binding site [chemical binding]; other site 399804008569 Mg2+ binding site [ion binding]; other site 399804008570 G-X-G motif; other site 399804008571 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 399804008572 active site 399804008573 phosphorylation site [posttranslational modification] 399804008574 intermolecular recognition site; other site 399804008575 dimerization interface [polypeptide binding]; other site 399804008576 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 399804008577 putative binding surface; other site 399804008578 active site 399804008579 Protein of unknown function (DUF416); Region: DUF416; pfam04222 399804008580 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804008581 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804008582 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 399804008583 putative effector binding pocket; other site 399804008584 dimerization interface [polypeptide binding]; other site 399804008585 Predicted permeases [General function prediction only]; Region: COG0679 399804008586 recombination and repair protein; Provisional; Region: PRK10869 399804008587 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 399804008588 Walker A/P-loop; other site 399804008589 ATP binding site [chemical binding]; other site 399804008590 Q-loop/lid; other site 399804008591 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 399804008592 ABC transporter signature motif; other site 399804008593 Walker B; other site 399804008594 D-loop; other site 399804008595 H-loop/switch region; other site 399804008596 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 399804008597 tetramer interfaces [polypeptide binding]; other site 399804008598 binuclear metal-binding site [ion binding]; other site 399804008599 thiamine monophosphate kinase; Provisional; Region: PRK05731 399804008600 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 399804008601 ATP binding site [chemical binding]; other site 399804008602 dimerization interface [polypeptide binding]; other site 399804008603 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 399804008604 putative RNA binding site [nucleotide binding]; other site 399804008605 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 399804008606 homopentamer interface [polypeptide binding]; other site 399804008607 active site 399804008608 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 399804008609 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 399804008610 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 399804008611 dimerization interface [polypeptide binding]; other site 399804008612 active site 399804008613 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 399804008614 Lumazine binding domain; Region: Lum_binding; pfam00677 399804008615 Lumazine binding domain; Region: Lum_binding; pfam00677 399804008616 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 399804008617 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 399804008618 catalytic motif [active] 399804008619 Zn binding site [ion binding]; other site 399804008620 RibD C-terminal domain; Region: RibD_C; cl17279 399804008621 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 399804008622 ATP cone domain; Region: ATP-cone; pfam03477 399804008623 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 399804008624 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 399804008625 dimer interface [polypeptide binding]; other site 399804008626 active site 399804008627 glycine-pyridoxal phosphate binding site [chemical binding]; other site 399804008628 folate binding site [chemical binding]; other site 399804008629 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 399804008630 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804008631 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804008632 ABC transporter; Region: ABC_tran_2; pfam12848 399804008633 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804008634 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804008635 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804008636 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 399804008637 putative effector binding pocket; other site 399804008638 dimerization interface [polypeptide binding]; other site 399804008639 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 399804008640 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 399804008641 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 399804008642 catalytic residues [active] 399804008643 Ketosteroid isomerase-related protein [General function prediction only]; Region: COG3631 399804008644 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804008645 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804008646 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804008647 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804008648 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 399804008649 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 399804008650 putative substrate translocation pore; other site 399804008651 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 399804008652 Helix-turn-helix domain; Region: HTH_18; pfam12833 399804008653 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804008654 Uncharacterized conserved protein [Function unknown]; Region: COG1432 399804008655 LabA_like proteins; Region: LabA_like/DUF88; cl10034 399804008656 putative metal binding site [ion binding]; other site 399804008657 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 399804008658 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804008659 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804008660 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804008661 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804008662 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804008663 OsmC-like protein; Region: OsmC; pfam02566 399804008664 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804008665 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804008666 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804008667 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 399804008668 dimerization interface [polypeptide binding]; other site 399804008669 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 399804008670 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 399804008671 GDP-binding site [chemical binding]; other site 399804008672 ACT binding site; other site 399804008673 IMP binding site; other site 399804008674 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 399804008675 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 399804008676 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 399804008677 active site 399804008678 phosphorylation site [posttranslational modification] 399804008679 intermolecular recognition site; other site 399804008680 dimerization interface [polypeptide binding]; other site 399804008681 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 399804008682 active site 399804008683 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804008684 metal binding site [ion binding]; metal-binding site 399804008685 active site 399804008686 I-site; other site 399804008687 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 399804008688 HDOD domain; Region: HDOD; pfam08668 399804008689 putative protease; Provisional; Region: PRK15452 399804008690 Peptidase family U32; Region: Peptidase_U32; pfam01136 399804008691 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 399804008692 SCP-2 sterol transfer family; Region: SCP2; cl01225 399804008693 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 399804008694 Peptidase family U32; Region: Peptidase_U32; pfam01136 399804008695 putative protease; Provisional; Region: PRK15447 399804008696 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 399804008697 Predicted membrane protein [Function unknown]; Region: COG3371 399804008698 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 399804008699 Nucleoside recognition; Region: Gate; pfam07670 399804008700 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 399804008701 putative active site [active] 399804008702 putative metal binding site [ion binding]; other site 399804008703 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 399804008704 putative acyl-acceptor binding pocket; other site 399804008705 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 399804008706 FOG: CBS domain [General function prediction only]; Region: COG0517 399804008707 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_24; cd04637 399804008708 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 399804008709 PilZ domain; Region: PilZ; pfam07238 399804008710 DNA repair protein RadA; Provisional; Region: PRK11823 399804008711 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 399804008712 Walker A motif/ATP binding site; other site 399804008713 ATP binding site [chemical binding]; other site 399804008714 Walker B motif; other site 399804008715 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 399804008716 PilZ domain; Region: PilZ; pfam07238 399804008717 PilZ domain; Region: PilZ; pfam07238 399804008718 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804008719 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 399804008720 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 399804008721 phosphoserine phosphatase SerB; Region: serB; TIGR00338 399804008722 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 399804008723 motif II; other site 399804008724 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 399804008725 purine nucleoside phosphorylase; Reviewed; Region: deoD; PRK05819 399804008726 phosphopentomutase; Provisional; Region: PRK05362 399804008727 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 399804008728 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 399804008729 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 399804008730 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 399804008731 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 399804008732 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 399804008733 intersubunit interface [polypeptide binding]; other site 399804008734 active site 399804008735 catalytic residue [active] 399804008736 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; pfam03502 399804008737 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 399804008738 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 399804008739 Nucleoside recognition; Region: Gate; pfam07670 399804008740 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 399804008741 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 399804008742 active site 399804008743 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 399804008744 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 399804008745 G1 box; other site 399804008746 putative GEF interaction site [polypeptide binding]; other site 399804008747 GTP/Mg2+ binding site [chemical binding]; other site 399804008748 Switch I region; other site 399804008749 G2 box; other site 399804008750 G3 box; other site 399804008751 Switch II region; other site 399804008752 G4 box; other site 399804008753 G5 box; other site 399804008754 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 399804008755 lipoprotein NlpI; Provisional; Region: PRK11189 399804008756 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 399804008757 binding surface 399804008758 TPR motif; other site 399804008759 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 399804008760 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 399804008761 RNase E interface [polypeptide binding]; other site 399804008762 trimer interface [polypeptide binding]; other site 399804008763 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 399804008764 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 399804008765 RNase E interface [polypeptide binding]; other site 399804008766 trimer interface [polypeptide binding]; other site 399804008767 active site 399804008768 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 399804008769 putative nucleic acid binding region [nucleotide binding]; other site 399804008770 G-X-X-G motif; other site 399804008771 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 399804008772 RNA binding site [nucleotide binding]; other site 399804008773 domain interface; other site 399804008774 biofilm formation regulator HmsP; Provisional; Region: PRK11829 399804008775 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804008776 metal binding site [ion binding]; metal-binding site 399804008777 active site 399804008778 I-site; other site 399804008779 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 399804008780 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 399804008781 16S/18S rRNA binding site [nucleotide binding]; other site 399804008782 S13e-L30e interaction site [polypeptide binding]; other site 399804008783 25S rRNA binding site [nucleotide binding]; other site 399804008784 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 399804008785 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 399804008786 RNA binding site [nucleotide binding]; other site 399804008787 active site 399804008788 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 399804008789 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 399804008790 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 399804008791 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 399804008792 translation initiation factor IF-2; Region: IF-2; TIGR00487 399804008793 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 399804008794 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 399804008795 G1 box; other site 399804008796 putative GEF interaction site [polypeptide binding]; other site 399804008797 GTP/Mg2+ binding site [chemical binding]; other site 399804008798 Switch I region; other site 399804008799 G2 box; other site 399804008800 G3 box; other site 399804008801 Switch II region; other site 399804008802 G4 box; other site 399804008803 G5 box; other site 399804008804 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 399804008805 Translation-initiation factor 2; Region: IF-2; pfam11987 399804008806 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 399804008807 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 399804008808 NusA N-terminal domain; Region: NusA_N; pfam08529 399804008809 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 399804008810 RNA binding site [nucleotide binding]; other site 399804008811 homodimer interface [polypeptide binding]; other site 399804008812 NusA-like KH domain; Region: KH_5; pfam13184 399804008813 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 399804008814 G-X-X-G motif; other site 399804008815 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 399804008816 ribosome maturation protein RimP; Reviewed; Region: PRK00092 399804008817 Sm and related proteins; Region: Sm_like; cl00259 399804008818 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 399804008819 putative oligomer interface [polypeptide binding]; other site 399804008820 putative RNA binding site [nucleotide binding]; other site 399804008821 Preprotein translocase SecG subunit; Region: SecG; pfam03840 399804008822 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 399804008823 triosephosphate isomerase; Provisional; Region: PRK14567 399804008824 substrate binding site [chemical binding]; other site 399804008825 dimer interface [polypeptide binding]; other site 399804008826 catalytic triad [active] 399804008827 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 399804008828 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 399804008829 active site 399804008830 substrate binding site [chemical binding]; other site 399804008831 metal binding site [ion binding]; metal-binding site 399804008832 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 399804008833 dihydropteroate synthase; Region: DHPS; TIGR01496 399804008834 substrate binding pocket [chemical binding]; other site 399804008835 dimer interface [polypeptide binding]; other site 399804008836 inhibitor binding site; inhibition site 399804008837 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 399804008838 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 399804008839 Walker A motif; other site 399804008840 ATP binding site [chemical binding]; other site 399804008841 Walker B motif; other site 399804008842 arginine finger; other site 399804008843 Peptidase family M41; Region: Peptidase_M41; pfam01434 399804008844 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 399804008845 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 399804008846 S-adenosylmethionine binding site [chemical binding]; other site 399804008847 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 399804008848 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13021 399804008849 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 399804008850 Protein export membrane protein; Region: SecD_SecF; pfam02355 399804008851 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 399804008852 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 399804008853 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 399804008854 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 399804008855 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 399804008856 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 399804008857 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 399804008858 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 399804008859 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 399804008860 GTP-binding protein YchF; Reviewed; Region: PRK09601 399804008861 YchF GTPase; Region: YchF; cd01900 399804008862 G1 box; other site 399804008863 GTP/Mg2+ binding site [chemical binding]; other site 399804008864 Switch I region; other site 399804008865 G2 box; other site 399804008866 Switch II region; other site 399804008867 G3 box; other site 399804008868 G4 box; other site 399804008869 G5 box; other site 399804008870 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 399804008871 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 399804008872 putative active site [active] 399804008873 catalytic residue [active] 399804008874 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 399804008875 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK08849 399804008876 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 399804008877 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 399804008878 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 399804008879 FeS/SAM binding site; other site 399804008880 TRAM domain; Region: TRAM; pfam01938 399804008881 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 399804008882 PhoH-like protein; Region: PhoH; pfam02562 399804008883 metal-binding heat shock protein; Provisional; Region: PRK00016 399804008884 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 399804008885 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 399804008886 Transporter associated domain; Region: CorC_HlyC; smart01091 399804008887 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 399804008888 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 399804008889 putative active site [active] 399804008890 catalytic triad [active] 399804008891 putative dimer interface [polypeptide binding]; other site 399804008892 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 399804008893 S-adenosylmethionine binding site [chemical binding]; other site 399804008894 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 399804008895 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 399804008896 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 399804008897 HIGH motif; other site 399804008898 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 399804008899 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 399804008900 active site 399804008901 KMSKS motif; other site 399804008902 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 399804008903 tRNA binding surface [nucleotide binding]; other site 399804008904 Lipopolysaccharide-assembly; Region: LptE; cl01125 399804008905 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 399804008906 DNA polymerase III, delta subunit; Region: holA; TIGR01128 399804008907 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 399804008908 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 399804008909 active site 399804008910 (T/H)XGH motif; other site 399804008911 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 399804008912 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 399804008913 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 399804008914 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 399804008915 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 399804008916 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 399804008917 Transglycosylase SLT domain; Region: SLT_2; pfam13406 399804008918 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 399804008919 N-acetyl-D-glucosamine binding site [chemical binding]; other site 399804008920 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 399804008921 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 399804008922 Sporulation related domain; Region: SPOR; pfam05036 399804008923 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 399804008924 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 399804008925 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 399804008926 hypothetical protein; Provisional; Region: PRK04998 399804008927 lipoate-protein ligase B; Provisional; Region: PRK14342 399804008928 lipoyl synthase; Provisional; Region: PRK05481 399804008929 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 399804008930 FeS/SAM binding site; other site 399804008931 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 399804008932 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804008933 Coenzyme A binding pocket [chemical binding]; other site 399804008934 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 399804008935 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 399804008936 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 399804008937 dimerization interface [polypeptide binding]; other site 399804008938 DPS ferroxidase diiron center [ion binding]; other site 399804008939 ion pore; other site 399804008940 Predicted membrane protein [Function unknown]; Region: COG3503 399804008941 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 399804008942 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 399804008943 N-terminal plug; other site 399804008944 ligand-binding site [chemical binding]; other site 399804008945 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 399804008946 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804008947 Integrase core domain; Region: rve; pfam00665 399804008948 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 399804008949 binding surface 399804008950 TPR motif; other site 399804008951 SWIM/SEC-C metal-binding motif protein, PBPRA1643 family; Region: SWIM_PBPRA1643; TIGR04102 399804008952 SEC-C motif; Region: SEC-C; pfam02810 399804008953 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 399804008954 catalytic site [active] 399804008955 putative active site [active] 399804008956 putative substrate binding site [chemical binding]; other site 399804008957 Protein of unknown function (DUF808); Region: DUF808; pfam05661 399804008958 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 399804008959 tetramer (dimer of dimers) interface [polypeptide binding]; other site 399804008960 active site 399804008961 dimer interface [polypeptide binding]; other site 399804008962 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 399804008963 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 399804008964 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 399804008965 putative RNA binding site [nucleotide binding]; other site 399804008966 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 399804008967 S-adenosylmethionine binding site [chemical binding]; other site 399804008968 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 399804008969 putative metal binding site [ion binding]; other site 399804008970 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 399804008971 putative catalytic site [active] 399804008972 putative phosphate binding site [ion binding]; other site 399804008973 putative metal binding site [ion binding]; other site 399804008974 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 399804008975 MgtE intracellular N domain; Region: MgtE_N; pfam03448 399804008976 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 399804008977 Divalent cation transporter; Region: MgtE; pfam01769 399804008978 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804008979 dimer interface [polypeptide binding]; other site 399804008980 putative CheW interface [polypeptide binding]; other site 399804008981 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 399804008982 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804008983 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 399804008984 substrate binding pocket [chemical binding]; other site 399804008985 membrane-bound complex binding site; other site 399804008986 hinge residues; other site 399804008987 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 399804008988 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 399804008989 active site 399804008990 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 399804008991 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 399804008992 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 399804008993 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 399804008994 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 399804008995 ATP-grasp domain; Region: ATP-grasp_4; cl17255 399804008996 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 399804008997 IMP binding site; other site 399804008998 dimer interface [polypeptide binding]; other site 399804008999 interdomain contacts; other site 399804009000 partial ornithine binding site; other site 399804009001 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 399804009002 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 399804009003 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 399804009004 catalytic site [active] 399804009005 subunit interface [polypeptide binding]; other site 399804009006 dihydrodipicolinate reductase; Provisional; Region: PRK00048 399804009007 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 399804009008 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 399804009009 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 399804009010 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 399804009011 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804009012 Peptidase family M48; Region: Peptidase_M48; pfam01435 399804009013 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 399804009014 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 399804009015 ATP binding site [chemical binding]; other site 399804009016 Mg++ binding site [ion binding]; other site 399804009017 motif III; other site 399804009018 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 399804009019 nucleotide binding region [chemical binding]; other site 399804009020 ATP-binding site [chemical binding]; other site 399804009021 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 399804009022 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 399804009023 dimer interface [polypeptide binding]; other site 399804009024 active site 399804009025 metal binding site [ion binding]; metal-binding site 399804009026 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 399804009027 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 399804009028 NAD(P) binding site [chemical binding]; other site 399804009029 catalytic residues [active] 399804009030 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 399804009031 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 399804009032 cobalamin binding residues [chemical binding]; other site 399804009033 putative BtuC binding residues; other site 399804009034 dimer interface [polypeptide binding]; other site 399804009035 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 399804009036 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804009037 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804009038 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804009039 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 399804009040 Putative transposase; Region: Y2_Tnp; pfam04986 399804009041 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 399804009042 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 399804009043 Int/Topo IB signature motif; other site 399804009044 integron integrase; Region: integrase_gron; TIGR02249 399804009045 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 399804009046 Int/Topo IB signature motif; other site 399804009047 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 399804009048 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 399804009049 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 399804009050 homodimer interface [polypeptide binding]; other site 399804009051 Walker A motif; other site 399804009052 ATP binding site [chemical binding]; other site 399804009053 hydroxycobalamin binding site [chemical binding]; other site 399804009054 Walker B motif; other site 399804009055 cobyric acid synthase; Provisional; Region: PRK00784 399804009056 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 399804009057 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 399804009058 catalytic triad [active] 399804009059 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 399804009060 homotrimer interface [polypeptide binding]; other site 399804009061 Walker A motif; other site 399804009062 GTP binding site [chemical binding]; other site 399804009063 Walker B motif; other site 399804009064 cobalamin synthase; Reviewed; Region: cobS; PRK00235 399804009065 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 399804009066 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 399804009067 putative dimer interface [polypeptide binding]; other site 399804009068 active site pocket [active] 399804009069 putative cataytic base [active] 399804009070 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 399804009071 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 399804009072 ABC-ATPase subunit interface; other site 399804009073 dimer interface [polypeptide binding]; other site 399804009074 putative PBP binding regions; other site 399804009075 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 399804009076 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 399804009077 Walker A/P-loop; other site 399804009078 ATP binding site [chemical binding]; other site 399804009079 Q-loop/lid; other site 399804009080 ABC transporter signature motif; other site 399804009081 Walker B; other site 399804009082 D-loop; other site 399804009083 H-loop/switch region; other site 399804009084 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 399804009085 catalytic core [active] 399804009086 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 399804009087 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 399804009088 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 399804009089 substrate binding pocket [chemical binding]; other site 399804009090 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 399804009091 B12 binding site [chemical binding]; other site 399804009092 cobalt ligand [ion binding]; other site 399804009093 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 399804009094 Domain of unknown function (DUF4263); Region: DUF4263; pfam14082 399804009095 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 399804009096 PAS domain; Region: PAS_9; pfam13426 399804009097 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 399804009098 PAS domain; Region: PAS_9; pfam13426 399804009099 putative active site [active] 399804009100 heme pocket [chemical binding]; other site 399804009101 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804009102 dimer interface [polypeptide binding]; other site 399804009103 putative CheW interface [polypeptide binding]; other site 399804009104 chaperone protein DnaJ; Provisional; Region: PRK10767 399804009105 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 399804009106 HSP70 interaction site [polypeptide binding]; other site 399804009107 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 399804009108 substrate binding site [polypeptide binding]; other site 399804009109 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 399804009110 Zn binding sites [ion binding]; other site 399804009111 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 399804009112 dimer interface [polypeptide binding]; other site 399804009113 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 399804009114 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 399804009115 nucleotide binding site [chemical binding]; other site 399804009116 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 399804009117 EamA-like transporter family; Region: EamA; pfam00892 399804009118 EamA-like transporter family; Region: EamA; pfam00892 399804009119 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 399804009120 putative deacylase active site [active] 399804009121 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 399804009122 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 399804009123 putative catalytic cysteine [active] 399804009124 gamma-glutamyl kinase; Provisional; Region: PRK05429 399804009125 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 399804009126 nucleotide binding site [chemical binding]; other site 399804009127 homotetrameric interface [polypeptide binding]; other site 399804009128 putative phosphate binding site [ion binding]; other site 399804009129 putative allosteric binding site; other site 399804009130 PUA domain; Region: PUA; pfam01472 399804009131 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 399804009132 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; pfam09904 399804009133 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 399804009134 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804009135 substrate binding pocket [chemical binding]; other site 399804009136 membrane-bound complex binding site; other site 399804009137 hinge residues; other site 399804009138 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 399804009139 Ligand Binding Site [chemical binding]; other site 399804009140 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 399804009141 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 399804009142 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 399804009143 NAD(P) binding site [chemical binding]; other site 399804009144 catalytic residues [active] 399804009145 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804009146 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804009147 Curli production assembly/transport component CsgG; Region: CsgG; pfam03783 399804009148 Type VIII secretion system (T8SS), CsgF protein; Region: CsgF; cl08082 399804009149 Curli assembly protein CsgE; Region: CsgE; pfam10627 399804009150 HAMP domain; Region: HAMP; pfam00672 399804009151 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 399804009152 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 399804009153 ATP binding site [chemical binding]; other site 399804009154 Mg2+ binding site [ion binding]; other site 399804009155 G-X-G motif; other site 399804009156 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 399804009157 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 399804009158 active site 399804009159 phosphorylation site [posttranslational modification] 399804009160 intermolecular recognition site; other site 399804009161 dimerization interface [polypeptide binding]; other site 399804009162 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 399804009163 Walker A motif; other site 399804009164 ATP binding site [chemical binding]; other site 399804009165 Walker B motif; other site 399804009166 arginine finger; other site 399804009167 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 399804009168 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 399804009169 FtsX-like permease family; Region: FtsX; pfam02687 399804009170 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 399804009171 FtsX-like permease family; Region: FtsX; pfam02687 399804009172 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 399804009173 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 399804009174 Walker A/P-loop; other site 399804009175 ATP binding site [chemical binding]; other site 399804009176 Q-loop/lid; other site 399804009177 ABC transporter signature motif; other site 399804009178 Walker B; other site 399804009179 D-loop; other site 399804009180 H-loop/switch region; other site 399804009181 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804009182 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804009183 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804009184 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 399804009185 active site 399804009186 substrate binding pocket [chemical binding]; other site 399804009187 dimer interface [polypeptide binding]; other site 399804009188 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 399804009189 FRG domain; Region: FRG; pfam08867 399804009190 glutamate racemase; Provisional; Region: PRK00865 399804009191 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804009192 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804009193 Coenzyme A binding pocket [chemical binding]; other site 399804009194 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 399804009195 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804009196 DNA-binding site [nucleotide binding]; DNA binding site 399804009197 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 399804009198 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804009199 homodimer interface [polypeptide binding]; other site 399804009200 catalytic residue [active] 399804009201 MAPEG family; Region: MAPEG; cl09190 399804009202 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 399804009203 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804009204 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 399804009205 CoenzymeA binding site [chemical binding]; other site 399804009206 subunit interaction site [polypeptide binding]; other site 399804009207 PHB binding site; other site 399804009208 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 399804009209 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 399804009210 generic binding surface II; other site 399804009211 generic binding surface I; other site 399804009212 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 399804009213 putative catalytic site [active] 399804009214 putative metal binding site [ion binding]; other site 399804009215 putative phosphate binding site [ion binding]; other site 399804009216 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10902 399804009217 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 399804009218 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804009219 FOG: WD40 repeat [General function prediction only]; Region: COG2319 399804009220 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 399804009221 structural tetrad; other site 399804009222 SlyX; Region: SlyX; pfam04102 399804009223 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 399804009224 active site 399804009225 catalytic residues [active] 399804009226 metal binding site [ion binding]; metal-binding site 399804009227 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 399804009228 uncharacterized proteobacterial lipoprotein; Region: lp_; TIGR02722 399804009229 aminopeptidase N, Streptomyces lividans type; Region: pepN_strep_liv; TIGR02412 399804009230 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_3; cd09602 399804009231 Zn binding site [ion binding]; other site 399804009232 Cache domain; Region: Cache_1; pfam02743 399804009233 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 399804009234 dimerization interface [polypeptide binding]; other site 399804009235 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804009236 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804009237 dimer interface [polypeptide binding]; other site 399804009238 putative CheW interface [polypeptide binding]; other site 399804009239 PAS domain S-box; Region: sensory_box; TIGR00229 399804009240 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 399804009241 putative active site [active] 399804009242 heme pocket [chemical binding]; other site 399804009243 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 399804009244 GAF domain; Region: GAF; pfam01590 399804009245 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804009246 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804009247 metal binding site [ion binding]; metal-binding site 399804009248 active site 399804009249 I-site; other site 399804009250 Protein of unknown function DUF72; Region: DUF72; cl00777 399804009251 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 399804009252 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 399804009253 Cupin domain; Region: Cupin_2; cl17218 399804009254 Helix-turn-helix domain; Region: HTH_18; pfam12833 399804009255 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 399804009256 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 399804009257 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 399804009258 catalytic triad [active] 399804009259 Periplasmic glucans biosynthesis protein [Inorganic ion transport and metabolism]; Region: MdoG; COG3131 399804009260 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 399804009261 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 399804009262 Carbon starvation protein CstA; Region: CstA; pfam02554 399804009263 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 399804009264 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 399804009265 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 399804009266 LrgB-like family; Region: LrgB; pfam04172 399804009267 LrgA family; Region: LrgA; pfam03788 399804009268 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 399804009269 G4 box; other site 399804009270 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804009271 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804009272 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 399804009273 putative dimerization interface [polypeptide binding]; other site 399804009274 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 399804009275 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 399804009276 substrate binding pocket [chemical binding]; other site 399804009277 membrane-bound complex binding site; other site 399804009278 hinge residues; other site 399804009279 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 399804009280 dimer interface [polypeptide binding]; other site 399804009281 conserved gate region; other site 399804009282 putative PBP binding loops; other site 399804009283 ABC-ATPase subunit interface; other site 399804009284 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 399804009285 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 399804009286 Walker A/P-loop; other site 399804009287 ATP binding site [chemical binding]; other site 399804009288 Q-loop/lid; other site 399804009289 ABC transporter signature motif; other site 399804009290 Walker B; other site 399804009291 D-loop; other site 399804009292 H-loop/switch region; other site 399804009293 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 399804009294 FMN binding site [chemical binding]; other site 399804009295 dimer interface [polypeptide binding]; other site 399804009296 DNA-J related protein; Region: DNAJ_related; pfam12339 399804009297 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 399804009298 HSP70 interaction site [polypeptide binding]; other site 399804009299 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 399804009300 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 399804009301 catalytic residues [active] 399804009302 hinge region; other site 399804009303 alpha helical domain; other site 399804009304 GlyGly-CTERM domain; Region: GlyGly_CTERM; TIGR03501 399804009305 Flavodoxin domain; Region: Flavodoxin_5; cl17428 399804009306 TIGR03899 family protein; Region: TIGR03899 399804009307 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 399804009308 ligand-binding site [chemical binding]; other site 399804009309 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 399804009310 TrkA-C domain; Region: TrkA_C; pfam02080 399804009311 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 399804009312 TrkA-C domain; Region: TrkA_C; pfam02080 399804009313 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 399804009314 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 399804009315 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 399804009316 CysD dimerization site [polypeptide binding]; other site 399804009317 G1 box; other site 399804009318 putative GEF interaction site [polypeptide binding]; other site 399804009319 GTP/Mg2+ binding site [chemical binding]; other site 399804009320 Switch I region; other site 399804009321 G2 box; other site 399804009322 G3 box; other site 399804009323 Switch II region; other site 399804009324 G4 box; other site 399804009325 G5 box; other site 399804009326 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 399804009327 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 399804009328 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 399804009329 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 399804009330 Active Sites [active] 399804009331 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 399804009332 active site 399804009333 SAM binding site [chemical binding]; other site 399804009334 homodimer interface [polypeptide binding]; other site 399804009335 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 399804009336 dimerization interface [polypeptide binding]; other site 399804009337 substrate binding site [chemical binding]; other site 399804009338 active site 399804009339 calcium binding site [ion binding]; other site 399804009340 Secreted phosphoprotein 24 (Spp-24); Region: Spp-24; pfam07448 399804009341 D-alanyl-D-alanine endopeptidase; Provisional; Region: pbpG; PRK11669 399804009342 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 399804009343 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 399804009344 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 399804009345 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 399804009346 dimer interface [polypeptide binding]; other site 399804009347 putative anticodon binding site; other site 399804009348 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 399804009349 motif 1; other site 399804009350 active site 399804009351 motif 2; other site 399804009352 motif 3; other site 399804009353 peptide chain release factor 2; Validated; Region: prfB; PRK00578 399804009354 This domain is found in peptide chain release factors; Region: PCRF; smart00937 399804009355 RF-1 domain; Region: RF-1; pfam00472 399804009356 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 399804009357 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 399804009358 catalytic loop [active] 399804009359 iron binding site [ion binding]; other site 399804009360 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 399804009361 4Fe-4S binding domain; Region: Fer4_6; pfam12837 399804009362 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 399804009363 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 399804009364 [4Fe-4S] binding site [ion binding]; other site 399804009365 molybdopterin cofactor binding site; other site 399804009366 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 399804009367 molybdopterin cofactor binding site; other site 399804009368 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 399804009369 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 399804009370 dimerization interface [polypeptide binding]; other site 399804009371 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804009372 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804009373 dimer interface [polypeptide binding]; other site 399804009374 putative CheW interface [polypeptide binding]; other site 399804009375 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 399804009376 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 399804009377 Chromate transporter; Region: Chromate_transp; pfam02417 399804009378 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 399804009379 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 399804009380 S-adenosylmethionine binding site [chemical binding]; other site 399804009381 FAD dependent oxidoreductase; Region: DAO; pfam01266 399804009382 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 399804009383 MarR family; Region: MarR; pfam01047 399804009384 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 399804009385 Predicted ATPase [General function prediction only]; Region: COG3903 399804009386 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 399804009387 Transglycosylase; Region: Transgly; cl17702 399804009388 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 399804009389 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 399804009390 Active Sites [active] 399804009391 sulfite reductase subunit beta; Provisional; Region: PRK13504 399804009392 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 399804009393 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 399804009394 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 399804009395 Flavodoxin; Region: Flavodoxin_1; pfam00258 399804009396 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 399804009397 FAD binding pocket [chemical binding]; other site 399804009398 FAD binding motif [chemical binding]; other site 399804009399 catalytic residues [active] 399804009400 NAD binding pocket [chemical binding]; other site 399804009401 phosphate binding motif [ion binding]; other site 399804009402 beta-alpha-beta structure motif; other site 399804009403 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 399804009404 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 399804009405 ligand binding site [chemical binding]; other site 399804009406 homodimer interface [polypeptide binding]; other site 399804009407 NAD(P) binding site [chemical binding]; other site 399804009408 trimer interface B [polypeptide binding]; other site 399804009409 trimer interface A [polypeptide binding]; other site 399804009410 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 399804009411 pyridine nucleotide transhydrogenase; Provisional; Region: pntB; PRK09444 399804009412 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 399804009413 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804009414 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 399804009415 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 399804009416 putative ribose interaction site [chemical binding]; other site 399804009417 putative ADP binding site [chemical binding]; other site 399804009418 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 399804009419 active site 399804009420 HIGH motif; other site 399804009421 nucleotide binding site [chemical binding]; other site 399804009422 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 399804009423 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 399804009424 putative acyl-acceptor binding pocket; other site 399804009425 potassium/proton antiporter; Reviewed; Region: PRK05326 399804009426 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 399804009427 TrkA-C domain; Region: TrkA_C; pfam02080 399804009428 Transporter associated domain; Region: CorC_HlyC; smart01091 399804009429 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 399804009430 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 399804009431 GAF domain; Region: GAF; pfam01590 399804009432 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 399804009433 Walker A motif; other site 399804009434 ATP binding site [chemical binding]; other site 399804009435 Walker B motif; other site 399804009436 arginine finger; other site 399804009437 L,D-transpeptidase; Provisional; Region: PRK10260 399804009438 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804009439 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 399804009440 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 399804009441 putative active site [active] 399804009442 Zn binding site [ion binding]; other site 399804009443 Predicted ATPase [General function prediction only]; Region: COG1485 399804009444 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804009445 Walker A/P-loop; other site 399804009446 ATP binding site [chemical binding]; other site 399804009447 ABC transporter signature motif; other site 399804009448 Walker B; other site 399804009449 D-loop; other site 399804009450 H-loop/switch region; other site 399804009451 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 399804009452 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 399804009453 active site 399804009454 phosphorylation site [posttranslational modification] 399804009455 intermolecular recognition site; other site 399804009456 dimerization interface [polypeptide binding]; other site 399804009457 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 399804009458 DNA binding site [nucleotide binding] 399804009459 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 399804009460 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 399804009461 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 399804009462 Ligand Binding Site [chemical binding]; other site 399804009463 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 399804009464 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 399804009465 dimer interface [polypeptide binding]; other site 399804009466 phosphorylation site [posttranslational modification] 399804009467 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 399804009468 ATP binding site [chemical binding]; other site 399804009469 Mg2+ binding site [ion binding]; other site 399804009470 G-X-G motif; other site 399804009471 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 399804009472 K+-transporting ATPase, c chain; Region: KdpC; cl00944 399804009473 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 399804009474 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 399804009475 Soluble P-type ATPase [General function prediction only]; Region: COG4087 399804009476 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 399804009477 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804009478 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804009479 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 399804009480 dimerization interface [polypeptide binding]; other site 399804009481 Domain of unknown function (DUF897); Region: DUF897; pfam05982 399804009482 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 399804009483 GAF domain; Region: GAF; pfam01590 399804009484 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804009485 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804009486 metal binding site [ion binding]; metal-binding site 399804009487 active site 399804009488 I-site; other site 399804009489 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 399804009490 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 399804009491 metal binding triad; other site 399804009492 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 399804009493 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 399804009494 metal binding triad; other site 399804009495 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 399804009496 spermidine synthase; Provisional; Region: PRK03612 399804009497 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 399804009498 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; pfam09938 399804009499 Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]; Region: PspA; COG1842 399804009500 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 399804009501 Ion channel; Region: Ion_trans_2; pfam07885 399804009502 Uncharacterized conserved protein [Function unknown]; Region: COG3025 399804009503 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 399804009504 putative active site [active] 399804009505 putative metal binding residues [ion binding]; other site 399804009506 signature motif; other site 399804009507 putative triphosphate binding site [ion binding]; other site 399804009508 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 399804009509 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 399804009510 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 399804009511 Bacterial SH3 domain homologues; Region: SH3b; smart00287 399804009512 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 399804009513 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 399804009514 Proline dehydrogenase; Region: Pro_dh; pfam01619 399804009515 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 399804009516 Glutamate binding site [chemical binding]; other site 399804009517 NAD binding site [chemical binding]; other site 399804009518 catalytic residues [active] 399804009519 Protein of unknown function, DUF599; Region: DUF599; pfam04654 399804009520 Helix-turn-helix domain; Region: HTH_17; pfam12728 399804009521 Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily; Region: CYTH-like_AC_IV-like; cd07890 399804009522 putative active site [active] 399804009523 putative metal binding residues [ion binding]; other site 399804009524 signature motif; other site 399804009525 putative triphosphate binding site [ion binding]; other site 399804009526 dimer interface [polypeptide binding]; other site 399804009527 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 399804009528 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 399804009529 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804009530 Walker A/P-loop; other site 399804009531 ATP binding site [chemical binding]; other site 399804009532 Q-loop/lid; other site 399804009533 ABC transporter signature motif; other site 399804009534 Walker B; other site 399804009535 D-loop; other site 399804009536 H-loop/switch region; other site 399804009537 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 399804009538 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 399804009539 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804009540 Walker A/P-loop; other site 399804009541 ATP binding site [chemical binding]; other site 399804009542 Q-loop/lid; other site 399804009543 ABC transporter signature motif; other site 399804009544 Walker B; other site 399804009545 D-loop; other site 399804009546 H-loop/switch region; other site 399804009547 Protein of unknown function (DUF3626); Region: DUF3626; pfam12294 399804009548 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 399804009549 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 399804009550 ATP binding site [chemical binding]; other site 399804009551 Mg++ binding site [ion binding]; other site 399804009552 motif III; other site 399804009553 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 399804009554 nucleotide binding region [chemical binding]; other site 399804009555 ATP-binding site [chemical binding]; other site 399804009556 PAS domain; Region: PAS_9; pfam13426 399804009557 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 399804009558 putative active site [active] 399804009559 heme pocket [chemical binding]; other site 399804009560 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804009561 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804009562 dimer interface [polypeptide binding]; other site 399804009563 putative CheW interface [polypeptide binding]; other site 399804009564 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 399804009565 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 399804009566 ATP binding site [chemical binding]; other site 399804009567 Mg++ binding site [ion binding]; other site 399804009568 motif III; other site 399804009569 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 399804009570 nucleotide binding region [chemical binding]; other site 399804009571 ATP-binding site [chemical binding]; other site 399804009572 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 399804009573 putative RNA binding site [nucleotide binding]; other site 399804009574 Pirin-related protein [General function prediction only]; Region: COG1741 399804009575 Pirin; Region: Pirin; pfam02678 399804009576 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 399804009577 Homeodomain-like domain; Region: HTH_23; pfam13384 399804009578 Winged helix-turn helix; Region: HTH_29; pfam13551 399804009579 Winged helix-turn helix; Region: HTH_33; pfam13592 399804009580 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804009581 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804009582 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 399804009583 Probable metal-binding protein (DUF2387); Region: DUF2387; pfam09526 399804009584 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 399804009585 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804009586 Walker A/P-loop; other site 399804009587 ATP binding site [chemical binding]; other site 399804009588 Q-loop/lid; other site 399804009589 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804009590 ABC transporter; Region: ABC_tran_2; pfam12848 399804009591 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 399804009592 Protein of unknown function (DUF2390); Region: DUF2390; pfam09523 399804009593 Uncharacterized conserved protein [Function unknown]; Region: COG3791 399804009594 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 399804009595 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 399804009596 putative hydrolase; Provisional; Region: PRK10985 399804009597 Uncharacterized protein family (UPF0270); Region: UPF0270; pfam06794 399804009598 phosphoribulokinase; Provisional; Region: PRK15453 399804009599 active site 399804009600 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 399804009601 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804009602 Coenzyme A binding pocket [chemical binding]; other site 399804009603 aminopeptidase B; Provisional; Region: PRK05015 399804009604 Peptidase; Region: DUF3663; pfam12404 399804009605 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 399804009606 interface (dimer of trimers) [polypeptide binding]; other site 399804009607 Substrate-binding/catalytic site; other site 399804009608 Zn-binding sites [ion binding]; other site 399804009609 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 399804009610 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 399804009611 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 399804009612 tRNA synthetases class I (E and Q), catalytic domain; Region: tRNA-synt_1c; pfam00749 399804009613 active site 399804009614 HIGH motif; other site 399804009615 nucleotide binding site [chemical binding]; other site 399804009616 active site 399804009617 KMSKS motif; other site 399804009618 poly(A) polymerase; Region: pcnB; TIGR01942 399804009619 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 399804009620 active site 399804009621 NTP binding site [chemical binding]; other site 399804009622 metal binding triad [ion binding]; metal-binding site 399804009623 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 399804009624 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 399804009625 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 399804009626 catalytic center binding site [active] 399804009627 ATP binding site [chemical binding]; other site 399804009628 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 399804009629 oligomerization interface [polypeptide binding]; other site 399804009630 active site 399804009631 metal binding site [ion binding]; metal-binding site 399804009632 Pantoate-beta-alanine ligase; Region: PanC; cd00560 399804009633 pantoate--beta-alanine ligase; Region: panC; TIGR00018 399804009634 active site 399804009635 ATP-binding site [chemical binding]; other site 399804009636 pantoate-binding site; other site 399804009637 HXXH motif; other site 399804009638 Curlin associated repeat; Region: Curlin_rpt; pfam07012 399804009639 Curlin associated repeat; Region: Curlin_rpt; pfam07012 399804009640 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 399804009641 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 399804009642 major curlin subunit; Provisional; Region: csgA; PRK10051 399804009643 Curlin associated repeat; Region: Curlin_rpt; pfam07012 399804009644 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 399804009645 Curlin associated repeat; Region: Curlin_rpt; pfam07012 399804009646 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 399804009647 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 399804009648 DNA binding residues [nucleotide binding] 399804009649 dimerization interface [polypeptide binding]; other site 399804009650 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 399804009651 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 399804009652 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 399804009653 ligand binding site [chemical binding]; other site 399804009654 NAD binding site [chemical binding]; other site 399804009655 tetramer interface [polypeptide binding]; other site 399804009656 catalytic site [active] 399804009657 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 399804009658 L-serine binding site [chemical binding]; other site 399804009659 ACT domain interface; other site 399804009660 putative global regulator; Reviewed; Region: PRK09559 399804009661 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 399804009662 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 399804009663 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804009664 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 399804009665 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 399804009666 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 399804009667 active site 399804009668 phosphorylation site [posttranslational modification] 399804009669 intermolecular recognition site; other site 399804009670 dimerization interface [polypeptide binding]; other site 399804009671 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804009672 Zn2+ binding site [ion binding]; other site 399804009673 Mg2+ binding site [ion binding]; other site 399804009674 Domain of unknown function (DUF4185); Region: DUF4185; pfam13810 399804009675 PAS domain; Region: PAS_9; pfam13426 399804009676 PAS domain S-box; Region: sensory_box; TIGR00229 399804009677 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 399804009678 putative active site [active] 399804009679 heme pocket [chemical binding]; other site 399804009680 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 399804009681 PAS fold; Region: PAS_3; pfam08447 399804009682 putative active site [active] 399804009683 heme pocket [chemical binding]; other site 399804009684 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 399804009685 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 399804009686 putative active site [active] 399804009687 heme pocket [chemical binding]; other site 399804009688 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 399804009689 putative active site [active] 399804009690 heme pocket [chemical binding]; other site 399804009691 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804009692 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 399804009693 dimer interface [polypeptide binding]; other site 399804009694 phosphorylation site [posttranslational modification] 399804009695 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 399804009696 ATP binding site [chemical binding]; other site 399804009697 Mg2+ binding site [ion binding]; other site 399804009698 G-X-G motif; other site 399804009699 Response regulator receiver domain; Region: Response_reg; pfam00072 399804009700 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 399804009701 active site 399804009702 phosphorylation site [posttranslational modification] 399804009703 intermolecular recognition site; other site 399804009704 dimerization interface [polypeptide binding]; other site 399804009705 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 399804009706 Response regulator receiver domain; Region: Response_reg; pfam00072 399804009707 active site 399804009708 phosphorylation site [posttranslational modification] 399804009709 intermolecular recognition site; other site 399804009710 dimerization interface [polypeptide binding]; other site 399804009711 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 399804009712 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 399804009713 amino acid carrier protein; Region: agcS; TIGR00835 399804009714 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 399804009715 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 399804009716 Walker A/P-loop; other site 399804009717 ATP binding site [chemical binding]; other site 399804009718 Q-loop/lid; other site 399804009719 ABC transporter signature motif; other site 399804009720 Walker B; other site 399804009721 D-loop; other site 399804009722 H-loop/switch region; other site 399804009723 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 399804009724 FtsX-like permease family; Region: FtsX; pfam02687 399804009725 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 399804009726 NapD protein; Region: NapD; pfam03927 399804009727 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 399804009728 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 399804009729 [4Fe-4S] binding site [ion binding]; other site 399804009730 molybdopterin cofactor binding site; other site 399804009731 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 399804009732 molybdopterin cofactor binding site; other site 399804009733 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 399804009734 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 399804009735 4Fe-4S binding domain; Region: Fer4_5; pfam12801 399804009736 4Fe-4S binding domain; Region: Fer4_5; pfam12801 399804009737 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 399804009738 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 399804009739 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804009740 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 399804009741 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804009742 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804009743 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 399804009744 putative dimerization interface [polypeptide binding]; other site 399804009745 elongation factor G; Reviewed; Region: PRK00007 399804009746 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 399804009747 G1 box; other site 399804009748 putative GEF interaction site [polypeptide binding]; other site 399804009749 GTP/Mg2+ binding site [chemical binding]; other site 399804009750 Switch I region; other site 399804009751 G2 box; other site 399804009752 G3 box; other site 399804009753 Switch II region; other site 399804009754 G4 box; other site 399804009755 G5 box; other site 399804009756 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 399804009757 Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily...; Region: EFG_like_IV; cl02789 399804009758 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 399804009759 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804009760 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 399804009761 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 399804009762 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 399804009763 ATP-grasp domain; Region: ATP-grasp_4; cl17255 399804009764 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 399804009765 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 399804009766 carboxyltransferase (CT) interaction site; other site 399804009767 biotinylation site [posttranslational modification]; other site 399804009768 LysR family transcriptional regulator; Provisional; Region: PRK14997 399804009769 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804009770 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 399804009771 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 399804009772 putative effector binding pocket; other site 399804009773 dimerization interface [polypeptide binding]; other site 399804009774 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 399804009775 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cl00237 399804009776 putative substrate binding pocket [chemical binding]; other site 399804009777 AC domain interface; other site 399804009778 catalytic triad [active] 399804009779 AB domain interface; other site 399804009780 hypothetical protein; Provisional; Region: PRK04860 399804009781 Zn-dependent metalloprotease, SprT family [General function prediction only]; Region: SprT; COG3091 399804009782 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 399804009783 Transposase DDE domain group 1; Region: DDE_Tnp_1_4; pfam13701 399804009784 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 399804009785 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 399804009786 Walker A/P-loop; other site 399804009787 ATP binding site [chemical binding]; other site 399804009788 Q-loop/lid; other site 399804009789 ABC transporter signature motif; other site 399804009790 Walker B; other site 399804009791 D-loop; other site 399804009792 H-loop/switch region; other site 399804009793 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 399804009794 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 399804009795 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 399804009796 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 399804009797 dimer interface [polypeptide binding]; other site 399804009798 conserved gate region; other site 399804009799 putative PBP binding loops; other site 399804009800 ABC-ATPase subunit interface; other site 399804009801 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 399804009802 Thermostable Phosphite Dehydrogenase; Region: PTDH; cd12157 399804009803 homodimer interface [polypeptide binding]; other site 399804009804 ligand binding site [chemical binding]; other site 399804009805 NAD binding site [chemical binding]; other site 399804009806 catalytic site [active] 399804009807 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804009808 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804009809 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 399804009810 dimerization interface [polypeptide binding]; other site 399804009811 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 399804009812 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804009813 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 399804009814 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804009815 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804009816 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804009817 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804009818 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 399804009819 Transposase; Region: HTH_Tnp_1; pfam01527 399804009820 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 399804009821 Transposase; Region: HTH_Tnp_1; pfam01527 399804009822 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 399804009823 putative transposase OrfB; Reviewed; Region: PHA02517 399804009824 HTH-like domain; Region: HTH_21; pfam13276 399804009825 Integrase core domain; Region: rve; pfam00665 399804009826 Integrase core domain; Region: rve_2; pfam13333 399804009827 Homeodomain-like domain; Region: HTH_23; pfam13384 399804009828 Winged helix-turn helix; Region: HTH_29; pfam13551 399804009829 Winged helix-turn helix; Region: HTH_33; pfam13592 399804009830 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804009831 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804009832 Transposase; Region: HTH_Tnp_1; pfam01527 399804009833 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 399804009834 putative transposase OrfB; Reviewed; Region: PHA02517 399804009835 HTH-like domain; Region: HTH_21; pfam13276 399804009836 Integrase core domain; Region: rve; pfam00665 399804009837 Integrase core domain; Region: rve_2; pfam13333 399804009838 RNA methyltransferase, RsmE family; Region: TIGR00046 399804009839 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 399804009840 glutathione synthetase; Provisional; Region: PRK05246 399804009841 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 399804009842 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 399804009843 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 399804009844 dimer interface [polypeptide binding]; other site 399804009845 Alkaline phosphatase homologues; Region: alkPPc; smart00098 399804009846 active site 399804009847 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 399804009848 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 399804009849 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 399804009850 S-adenosylmethionine binding site [chemical binding]; other site 399804009851 Protein of unknown function (DUF342); Region: DUF342; pfam03961 399804009852 protein structure with unknown function; Region: DUF4144; pfam13642 399804009853 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_2; cd06160 399804009854 Peptidase family M50; Region: Peptidase_M50; pfam02163 399804009855 active site 399804009856 putative substrate binding region [chemical binding]; other site 399804009857 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804009858 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804009859 metal binding site [ion binding]; metal-binding site 399804009860 active site 399804009861 I-site; other site 399804009862 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 399804009863 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 399804009864 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 399804009865 Walker A/P-loop; other site 399804009866 ATP binding site [chemical binding]; other site 399804009867 Q-loop/lid; other site 399804009868 ABC transporter signature motif; other site 399804009869 Walker B; other site 399804009870 D-loop; other site 399804009871 H-loop/switch region; other site 399804009872 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 399804009873 FtsX-like permease family; Region: FtsX; pfam02687 399804009874 macrolide transporter subunit MacA; Provisional; Region: PRK11578 399804009875 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804009876 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804009877 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 399804009878 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 399804009879 THF binding site; other site 399804009880 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 399804009881 substrate binding site [chemical binding]; other site 399804009882 THF binding site; other site 399804009883 zinc-binding site [ion binding]; other site 399804009884 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804009885 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804009886 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 399804009887 putative dimerization interface [polypeptide binding]; other site 399804009888 HDOD domain; Region: HDOD; pfam08668 399804009889 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 399804009890 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 399804009891 N-terminal plug; other site 399804009892 ligand-binding site [chemical binding]; other site 399804009893 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 399804009894 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 399804009895 active site 399804009896 tetramer interface [polypeptide binding]; other site 399804009897 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 399804009898 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 399804009899 substrate binding site [chemical binding]; other site 399804009900 dimer interface [polypeptide binding]; other site 399804009901 ATP binding site [chemical binding]; other site 399804009902 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 399804009903 Protein of unknown function (DUF3103); Region: DUF3103; pfam11301 399804009904 Protein of unknown function (DUF3622); Region: DUF3622; pfam12286 399804009905 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 399804009906 active site 399804009907 PhoD-like phosphatase; Region: PhoD; pfam09423 399804009908 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 399804009909 putative active site [active] 399804009910 putative metal binding site [ion binding]; other site 399804009911 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 399804009912 FOG: CBS domain [General function prediction only]; Region: COG0517 399804009913 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 399804009914 Domain of unknown function (DUF4274); Region: DUF4274; pfam14096 399804009915 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 399804009916 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 399804009917 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 399804009918 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 399804009919 substrate binding pocket [chemical binding]; other site 399804009920 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 399804009921 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 399804009922 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804009923 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 399804009924 N-terminal plug; other site 399804009925 ligand-binding site [chemical binding]; other site 399804009926 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 399804009927 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 399804009928 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 399804009929 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 399804009930 Soluble P-type ATPase [General function prediction only]; Region: COG4087 399804009931 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 399804009932 YcaO domain protein; Region: TIGR03549 399804009933 OsmC-like protein; Region: OsmC; pfam02566 399804009934 YcaO-like family; Region: YcaO; pfam02624 399804009935 Cache domain; Region: Cache_2; pfam08269 399804009936 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 399804009937 dimerization interface [polypeptide binding]; other site 399804009938 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 399804009939 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804009940 dimer interface [polypeptide binding]; other site 399804009941 putative CheW interface [polypeptide binding]; other site 399804009942 Ribosome recycling factor; Region: RRF_GI; pfam12614 399804009943 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 399804009944 Nuclease-related domain; Region: NERD; pfam08378 399804009945 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804009946 AAA domain; Region: AAA_23; pfam13476 399804009947 Walker A/P-loop; other site 399804009948 ATP binding site [chemical binding]; other site 399804009949 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804009950 Q-loop/lid; other site 399804009951 ABC transporter signature motif; other site 399804009952 Walker B; other site 399804009953 D-loop; other site 399804009954 H-loop/switch region; other site 399804009955 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804009956 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804009957 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804009958 glycine dehydrogenase; Provisional; Region: PRK05367 399804009959 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 399804009960 tetramer interface [polypeptide binding]; other site 399804009961 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804009962 catalytic residue [active] 399804009963 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 399804009964 tetramer interface [polypeptide binding]; other site 399804009965 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804009966 catalytic residue [active] 399804009967 glycine cleavage system protein H; Provisional; Region: PRK13380 399804009968 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 399804009969 lipoyl attachment site [posttranslational modification]; other site 399804009970 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 399804009971 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 399804009972 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 399804009973 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 399804009974 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 399804009975 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 399804009976 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 399804009977 Cell division protein ZapA; Region: ZapA; pfam05164 399804009978 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 399804009979 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 399804009980 dihydromonapterin reductase; Provisional; Region: PRK06483 399804009981 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804009982 NAD(P) binding site [chemical binding]; other site 399804009983 active site 399804009984 Protein of unknown function, DUF393; Region: DUF393; pfam04134 399804009985 malate dehydrogenase; Provisional; Region: PRK05086 399804009986 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 399804009987 NAD binding site [chemical binding]; other site 399804009988 dimerization interface [polypeptide binding]; other site 399804009989 Substrate binding site [chemical binding]; other site 399804009990 arginine repressor; Provisional; Region: PRK05066 399804009991 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 399804009992 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 399804009993 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 399804009994 NADH(P)-binding; Region: NAD_binding_10; pfam13460 399804009995 NAD binding site [chemical binding]; other site 399804009996 substrate binding site [chemical binding]; other site 399804009997 putative active site [active] 399804009998 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804009999 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804010000 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 399804010001 putative effector binding pocket; other site 399804010002 dimerization interface [polypeptide binding]; other site 399804010003 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 399804010004 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 399804010005 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 399804010006 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 399804010007 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 399804010008 Walker A/P-loop; other site 399804010009 ATP binding site [chemical binding]; other site 399804010010 Q-loop/lid; other site 399804010011 ABC transporter signature motif; other site 399804010012 Walker B; other site 399804010013 D-loop; other site 399804010014 H-loop/switch region; other site 399804010015 TOBE domain; Region: TOBE_2; pfam08402 399804010016 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 399804010017 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 399804010018 dimer interface [polypeptide binding]; other site 399804010019 conserved gate region; other site 399804010020 putative PBP binding loops; other site 399804010021 ABC-ATPase subunit interface; other site 399804010022 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 399804010023 dimer interface [polypeptide binding]; other site 399804010024 conserved gate region; other site 399804010025 putative PBP binding loops; other site 399804010026 ABC-ATPase subunit interface; other site 399804010027 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 399804010028 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 399804010029 putative glutathione S-transferase; Provisional; Region: PRK10357 399804010030 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 399804010031 putative C-terminal domain interface [polypeptide binding]; other site 399804010032 putative GSH binding site (G-site) [chemical binding]; other site 399804010033 putative dimer interface [polypeptide binding]; other site 399804010034 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 399804010035 substrate binding pocket (H-site) [chemical binding]; other site 399804010036 N-terminal domain interface [polypeptide binding]; other site 399804010037 ferredoxin-NADP reductase; Provisional; Region: PRK10926 399804010038 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 399804010039 FAD binding pocket [chemical binding]; other site 399804010040 FAD binding motif [chemical binding]; other site 399804010041 phosphate binding motif [ion binding]; other site 399804010042 beta-alpha-beta structure motif; other site 399804010043 NAD binding pocket [chemical binding]; other site 399804010044 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 399804010045 catalytic core [active] 399804010046 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 399804010047 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 399804010048 active site 399804010049 FMN binding site [chemical binding]; other site 399804010050 substrate binding site [chemical binding]; other site 399804010051 3Fe-4S cluster binding site [ion binding]; other site 399804010052 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 399804010053 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 399804010054 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804010055 Walker A/P-loop; other site 399804010056 ATP binding site [chemical binding]; other site 399804010057 Q-loop/lid; other site 399804010058 ABC transporter signature motif; other site 399804010059 Walker B; other site 399804010060 D-loop; other site 399804010061 H-loop/switch region; other site 399804010062 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 399804010063 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 399804010064 probable ammonium transporter, marine subtype; Region: marine_trans_1; TIGR03644 399804010065 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 399804010066 Nitrogen regulatory protein P-II; Region: P-II; smart00938 399804010067 Isochorismatase family; Region: Isochorismatase; pfam00857 399804010068 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 399804010069 catalytic triad [active] 399804010070 dimer interface [polypeptide binding]; other site 399804010071 conserved cis-peptide bond; other site 399804010072 Protein of unknown function (DUF2999); Region: DUF2999; pfam11212 399804010073 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 399804010074 heme-binding site [chemical binding]; other site 399804010075 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010076 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010077 metal binding site [ion binding]; metal-binding site 399804010078 active site 399804010079 I-site; other site 399804010080 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 399804010081 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 399804010082 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 399804010083 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 399804010084 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 399804010085 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 399804010086 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 399804010087 DsbD alpha interface [polypeptide binding]; other site 399804010088 catalytic residues [active] 399804010089 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 399804010090 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 399804010091 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 399804010092 TrkA-N domain; Region: TrkA_N; pfam02254 399804010093 galactokinase; Provisional; Region: PRK05101 399804010094 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 399804010095 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 399804010096 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 399804010097 active site 399804010098 catalytic residues [active] 399804010099 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 399804010100 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 399804010101 NAD(P) binding site [chemical binding]; other site 399804010102 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 399804010103 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804010104 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804010105 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804010106 Leucine rich repeat; Region: LRR_8; pfam13855 399804010107 Leucine rich repeat; Region: LRR_8; pfam13855 399804010108 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 399804010109 active site 399804010110 ATP binding site [chemical binding]; other site 399804010111 substrate binding site [chemical binding]; other site 399804010112 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 399804010113 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 399804010114 N-acetyl-D-glucosamine binding site [chemical binding]; other site 399804010115 catalytic residue [active] 399804010116 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804010117 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804010118 Part of AAA domain; Region: AAA_19; pfam13245 399804010119 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 399804010120 AAA domain; Region: AAA_12; pfam13087 399804010121 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804010122 Coenzyme A binding pocket [chemical binding]; other site 399804010123 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 399804010124 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 399804010125 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 399804010126 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 399804010127 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 399804010128 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 399804010129 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 399804010130 stringent starvation protein A; Provisional; Region: sspA; PRK09481 399804010131 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 399804010132 C-terminal domain interface [polypeptide binding]; other site 399804010133 putative GSH binding site (G-site) [chemical binding]; other site 399804010134 dimer interface [polypeptide binding]; other site 399804010135 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 399804010136 dimer interface [polypeptide binding]; other site 399804010137 N-terminal domain interface [polypeptide binding]; other site 399804010138 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 399804010139 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 399804010140 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 399804010141 Qi binding site; other site 399804010142 intrachain domain interface; other site 399804010143 interchain domain interface [polypeptide binding]; other site 399804010144 heme bH binding site [chemical binding]; other site 399804010145 heme bL binding site [chemical binding]; other site 399804010146 Qo binding site; other site 399804010147 Cytochrome b(C-terminus)/b6/petD: 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_C; cd00290 399804010148 interchain domain interface [polypeptide binding]; other site 399804010149 intrachain domain interface; other site 399804010150 Qi binding site; other site 399804010151 Qo binding site; other site 399804010152 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 399804010153 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 399804010154 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 399804010155 [2Fe-2S] cluster binding site [ion binding]; other site 399804010156 HflC protein; Region: hflC; TIGR01932 399804010157 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 399804010158 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 399804010159 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 399804010160 HflK protein; Region: hflK; TIGR01933 399804010161 GTPase HflX; Provisional; Region: PRK11058 399804010162 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 399804010163 HflX GTPase family; Region: HflX; cd01878 399804010164 G1 box; other site 399804010165 GTP/Mg2+ binding site [chemical binding]; other site 399804010166 Switch I region; other site 399804010167 G2 box; other site 399804010168 G3 box; other site 399804010169 Switch II region; other site 399804010170 G4 box; other site 399804010171 G5 box; other site 399804010172 bacterial Hfq-like; Region: Hfq; cd01716 399804010173 hexamer interface [polypeptide binding]; other site 399804010174 Sm1 motif; other site 399804010175 RNA binding site [nucleotide binding]; other site 399804010176 Sm2 motif; other site 399804010177 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 399804010178 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 399804010179 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 399804010180 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 399804010181 ATP binding site [chemical binding]; other site 399804010182 Mg2+ binding site [ion binding]; other site 399804010183 G-X-G motif; other site 399804010184 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 399804010185 ATP binding site [chemical binding]; other site 399804010186 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 399804010187 N-acetylmuramoyl-l-alanine amidase II; Provisional; Region: PRK10431 399804010188 AMIN domain; Region: AMIN; pfam11741 399804010189 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 399804010190 active site 399804010191 metal binding site [ion binding]; metal-binding site 399804010192 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 399804010193 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 399804010194 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 399804010195 putative carbohydrate kinase; Provisional; Region: PRK10565 399804010196 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 399804010197 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 399804010198 putative substrate binding site [chemical binding]; other site 399804010199 putative ATP binding site [chemical binding]; other site 399804010200 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 399804010201 dinuclear metal binding motif [ion binding]; other site 399804010202 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 399804010203 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 399804010204 catalytic site [active] 399804010205 putative active site [active] 399804010206 putative substrate binding site [chemical binding]; other site 399804010207 dimer interface [polypeptide binding]; other site 399804010208 GTPase RsgA; Reviewed; Region: PRK12288 399804010209 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 399804010210 RNA binding site [nucleotide binding]; other site 399804010211 homodimer interface [polypeptide binding]; other site 399804010212 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 399804010213 GTPase/Zn-binding domain interface [polypeptide binding]; other site 399804010214 GTP/Mg2+ binding site [chemical binding]; other site 399804010215 G4 box; other site 399804010216 G5 box; other site 399804010217 G1 box; other site 399804010218 Switch I region; other site 399804010219 G2 box; other site 399804010220 G3 box; other site 399804010221 Switch II region; other site 399804010222 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 399804010223 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 399804010224 EamA-like transporter family; Region: EamA; pfam00892 399804010225 putative mechanosensitive channel protein; Provisional; Region: PRK10929 399804010226 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 399804010227 Mechanosensitive ion channel; Region: MS_channel; pfam00924 399804010228 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 399804010229 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 399804010230 active site 399804010231 catalytic site [active] 399804010232 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 399804010233 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 399804010234 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 399804010235 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 399804010236 S-adenosylmethionine binding site [chemical binding]; other site 399804010237 dihydroorotase; Provisional; Region: PRK01211 399804010238 Protein kinase domain; Region: Pkinase; pfam00069 399804010239 Catalytic domain of Protein Kinases; Region: PKc; cd00180 399804010240 active site 399804010241 ATP binding site [chemical binding]; other site 399804010242 substrate binding site [chemical binding]; other site 399804010243 activation loop (A-loop); other site 399804010244 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 399804010245 active site 399804010246 Cache domain; Region: Cache_1; pfam02743 399804010247 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 399804010248 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 399804010249 putative active site [active] 399804010250 heme pocket [chemical binding]; other site 399804010251 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 399804010252 putative active site [active] 399804010253 heme pocket [chemical binding]; other site 399804010254 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 399804010255 dimer interface [polypeptide binding]; other site 399804010256 phosphorylation site [posttranslational modification] 399804010257 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 399804010258 ATP binding site [chemical binding]; other site 399804010259 Mg2+ binding site [ion binding]; other site 399804010260 G-X-G motif; other site 399804010261 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 399804010262 Response regulator receiver domain; Region: Response_reg; pfam00072 399804010263 active site 399804010264 phosphorylation site [posttranslational modification] 399804010265 intermolecular recognition site; other site 399804010266 dimerization interface [polypeptide binding]; other site 399804010267 Response regulator receiver domain; Region: Response_reg; pfam00072 399804010268 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 399804010269 active site 399804010270 phosphorylation site [posttranslational modification] 399804010271 intermolecular recognition site; other site 399804010272 dimerization interface [polypeptide binding]; other site 399804010273 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 399804010274 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 399804010275 putative active site [active] 399804010276 PhoH-like protein; Region: PhoH; pfam02562 399804010277 ATP-dependent helicase HepA; Validated; Region: PRK04914 399804010278 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 399804010279 ATP binding site [chemical binding]; other site 399804010280 putative Mg++ binding site [ion binding]; other site 399804010281 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 399804010282 nucleotide binding region [chemical binding]; other site 399804010283 ATP-binding site [chemical binding]; other site 399804010284 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 399804010285 enoyl-CoA hydratase; Provisional; Region: PRK07509 399804010286 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 399804010287 substrate binding site [chemical binding]; other site 399804010288 oxyanion hole (OAH) forming residues; other site 399804010289 trimer interface [polypeptide binding]; other site 399804010290 Response regulator receiver domain; Region: Response_reg; pfam00072 399804010291 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 399804010292 active site 399804010293 phosphorylation site [posttranslational modification] 399804010294 intermolecular recognition site; other site 399804010295 dimerization interface [polypeptide binding]; other site 399804010296 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 399804010297 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 399804010298 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010299 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010300 metal binding site [ion binding]; metal-binding site 399804010301 active site 399804010302 I-site; other site 399804010303 RNase E inhibitor protein; Provisional; Region: PRK11191 399804010304 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 399804010305 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 399804010306 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 399804010307 putative acyl-acceptor binding pocket; other site 399804010308 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 399804010309 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 399804010310 Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_c; cd01145 399804010311 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 399804010312 putative ligand binding site [chemical binding]; other site 399804010313 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 399804010314 formate--tetrahydrofolate ligase; Provisional; Region: PRK13506 399804010315 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 399804010316 Potassium binding sites [ion binding]; other site 399804010317 Cesium cation binding sites [ion binding]; other site 399804010318 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 399804010319 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 399804010320 active site 2 [active] 399804010321 active site 1 [active] 399804010322 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 399804010323 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 399804010324 S-adenosylmethionine binding site [chemical binding]; other site 399804010325 TraB family; Region: TraB; pfam01963 399804010326 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 399804010327 FOG: CBS domain [General function prediction only]; Region: COG0517 399804010328 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 399804010329 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010330 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010331 metal binding site [ion binding]; metal-binding site 399804010332 active site 399804010333 I-site; other site 399804010334 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 399804010335 Protein of unknown function (DUF4240); Region: DUF4240; pfam14024 399804010336 Response regulator receiver domain; Region: Response_reg; pfam00072 399804010337 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 399804010338 active site 399804010339 phosphorylation site [posttranslational modification] 399804010340 intermolecular recognition site; other site 399804010341 dimerization interface [polypeptide binding]; other site 399804010342 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 399804010343 Response regulator receiver domain; Region: Response_reg; pfam00072 399804010344 active site 399804010345 phosphorylation site [posttranslational modification] 399804010346 intermolecular recognition site; other site 399804010347 dimerization interface [polypeptide binding]; other site 399804010348 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 399804010349 IHF dimer interface [polypeptide binding]; other site 399804010350 IHF - DNA interface [nucleotide binding]; other site 399804010351 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 399804010352 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 399804010353 ATP-grasp domain; Region: ATP-grasp_4; cl17255 399804010354 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 399804010355 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 399804010356 active site 399804010357 phosphorylation site [posttranslational modification] 399804010358 intermolecular recognition site; other site 399804010359 dimerization interface [polypeptide binding]; other site 399804010360 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010361 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010362 metal binding site [ion binding]; metal-binding site 399804010363 active site 399804010364 I-site; other site 399804010365 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 399804010366 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 399804010367 Response regulator receiver domain; Region: Response_reg; pfam00072 399804010368 active site 399804010369 phosphorylation site [posttranslational modification] 399804010370 intermolecular recognition site; other site 399804010371 CHASE domain; Region: CHASE; pfam03924 399804010372 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 399804010373 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 399804010374 putative active site [active] 399804010375 heme pocket [chemical binding]; other site 399804010376 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 399804010377 dimer interface [polypeptide binding]; other site 399804010378 phosphorylation site [posttranslational modification] 399804010379 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 399804010380 ATP binding site [chemical binding]; other site 399804010381 Mg2+ binding site [ion binding]; other site 399804010382 G-X-G motif; other site 399804010383 conserved hypothetical protein; Region: QEGLA; TIGR02421 399804010384 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 399804010385 amino acid carrier protein; Region: agcS; TIGR00835 399804010386 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 399804010387 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 399804010388 Beta-Casp domain; Region: Beta-Casp; smart01027 399804010389 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 399804010390 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 399804010391 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 399804010392 Uncharacterized conserved protein [Function unknown]; Region: COG1359 399804010393 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804010394 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 399804010395 Coenzyme A binding pocket [chemical binding]; other site 399804010396 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 399804010397 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 399804010398 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 399804010399 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804010400 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 399804010401 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804010402 Outer membrane efflux protein; Region: OEP; pfam02321 399804010403 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 399804010404 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 399804010405 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 399804010406 hypothetical protein; Provisional; Region: PRK09256 399804010407 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 399804010408 Dehydroquinase class II; Region: DHquinase_II; pfam01220 399804010409 active site 399804010410 trimer interface [polypeptide binding]; other site 399804010411 dimer interface [polypeptide binding]; other site 399804010412 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 399804010413 NAD(P) binding site [chemical binding]; other site 399804010414 active site 399804010415 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 399804010416 FMN reductase; Validated; Region: fre; PRK08051 399804010417 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 399804010418 FAD binding pocket [chemical binding]; other site 399804010419 FAD binding motif [chemical binding]; other site 399804010420 phosphate binding motif [ion binding]; other site 399804010421 beta-alpha-beta structure motif; other site 399804010422 NAD binding pocket [chemical binding]; other site 399804010423 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804010424 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804010425 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804010426 Domain of unknown function (DUF4411); Region: DUF4411; pfam14367 399804010427 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 399804010428 salt bridge; other site 399804010429 non-specific DNA binding site [nucleotide binding]; other site 399804010430 sequence-specific DNA binding site [nucleotide binding]; other site 399804010431 Domain of unknown function (DUF955); Region: DUF955; cl01076 399804010432 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 399804010433 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804010434 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 399804010435 DNA binding site [nucleotide binding] 399804010436 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 399804010437 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 399804010438 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 399804010439 Walker A/P-loop; other site 399804010440 ATP binding site [chemical binding]; other site 399804010441 Q-loop/lid; other site 399804010442 ABC transporter signature motif; other site 399804010443 Walker B; other site 399804010444 D-loop; other site 399804010445 H-loop/switch region; other site 399804010446 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 399804010447 NosL; Region: NosL; pfam05573 399804010448 TPR repeat; Region: TPR_11; pfam13414 399804010449 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 399804010450 binding surface 399804010451 TPR motif; other site 399804010452 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 399804010453 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 399804010454 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804010455 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 399804010456 active site residue [active] 399804010457 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 399804010458 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 399804010459 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 399804010460 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 399804010461 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 399804010462 catalytic residues [active] 399804010463 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs; Region: NTP-PPase_DR2231_like; cd11530 399804010464 metal binding site [ion binding]; metal-binding site 399804010465 Pathogenicity locus; Region: Cdd1; pfam11731 399804010466 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 399804010467 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 399804010468 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 399804010469 FMN binding site [chemical binding]; other site 399804010470 substrate binding site [chemical binding]; other site 399804010471 putative catalytic residue [active] 399804010472 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 399804010473 UbiA prenyltransferase family; Region: UbiA; pfam01040 399804010474 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 399804010475 Part of AAA domain; Region: AAA_19; pfam13245 399804010476 Family description; Region: UvrD_C_2; pfam13538 399804010477 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 399804010478 PIN domain; Region: PIN_3; pfam13470 399804010479 DNA binding domain, excisionase family; Region: excise; TIGR01764 399804010480 Methyltransferase domain; Region: Methyltransf_31; pfam13847 399804010481 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 399804010482 S-adenosylmethionine binding site [chemical binding]; other site 399804010483 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_21; cd04680 399804010484 nudix motif; other site 399804010485 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 399804010486 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 399804010487 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 399804010488 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 399804010489 substrate binding pocket [chemical binding]; other site 399804010490 membrane-bound complex binding site; other site 399804010491 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 399804010492 DctM-like transporters; Region: DctM; pfam06808 399804010493 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 399804010494 Transcriptional regulators [Transcription]; Region: FadR; COG2186 399804010495 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804010496 DNA-binding site [nucleotide binding]; DNA binding site 399804010497 FCD domain; Region: FCD; pfam07729 399804010498 outer membrane porin, OprD family; Region: OprD; pfam03573 399804010499 Tannase and feruloyl esterase; Region: Tannase; pfam07519 399804010500 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 399804010501 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 399804010502 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 399804010503 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804010504 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 399804010505 putative active site [active] 399804010506 PAS fold; Region: PAS_3; pfam08447 399804010507 heme pocket [chemical binding]; other site 399804010508 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010509 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010510 metal binding site [ion binding]; metal-binding site 399804010511 active site 399804010512 I-site; other site 399804010513 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 399804010514 thioredoxin 2; Provisional; Region: PRK10996 399804010515 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 399804010516 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 399804010517 catalytic residues [active] 399804010518 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 399804010519 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 399804010520 transmembrane helices; other site 399804010521 putative MFS family transporter protein; Provisional; Region: PRK03633 399804010522 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 399804010523 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 399804010524 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 399804010525 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 399804010526 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 399804010527 Predicted permease; Region: DUF318; cl17795 399804010528 Predicted permease; Region: DUF318; cl17795 399804010529 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 399804010530 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 399804010531 DNA binding residues [nucleotide binding] 399804010532 dimer interface [polypeptide binding]; other site 399804010533 metal binding site [ion binding]; metal-binding site 399804010534 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 399804010535 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 399804010536 purine monophosphate binding site [chemical binding]; other site 399804010537 dimer interface [polypeptide binding]; other site 399804010538 putative catalytic residues [active] 399804010539 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 399804010540 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 399804010541 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 399804010542 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 399804010543 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 399804010544 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 399804010545 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 399804010546 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_C39C; cd02419 399804010547 putative active site [active] 399804010548 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 399804010549 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 399804010550 Walker A/P-loop; other site 399804010551 ATP binding site [chemical binding]; other site 399804010552 Q-loop/lid; other site 399804010553 ABC transporter signature motif; other site 399804010554 Walker B; other site 399804010555 D-loop; other site 399804010556 H-loop/switch region; other site 399804010557 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 399804010558 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804010559 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1)-like, classical (c) SDRs; Region: 11beta-HSD1_like_SDR_c; cd05332 399804010560 short chain dehydrogenase; Provisional; Region: PRK06181 399804010561 NADP binding site [chemical binding]; other site 399804010562 homodimer interface [polypeptide binding]; other site 399804010563 substrate binding site [chemical binding]; other site 399804010564 active site 399804010565 PAS fold; Region: PAS_4; pfam08448 399804010566 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 399804010567 putative active site [active] 399804010568 heme pocket [chemical binding]; other site 399804010569 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010570 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010571 metal binding site [ion binding]; metal-binding site 399804010572 active site 399804010573 I-site; other site 399804010574 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 399804010575 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 399804010576 substrate binding site [chemical binding]; other site 399804010577 active site 399804010578 anti-RNA polymerase sigma 70 factor; Provisional; Region: PRK11718 399804010579 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 399804010580 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 399804010581 substrate binding site [chemical binding]; other site 399804010582 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 399804010583 substrate binding site [chemical binding]; other site 399804010584 ligand binding site [chemical binding]; other site 399804010585 2-deoxyglucose-6-phosphatase; Provisional; Region: PRK10826 399804010586 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 399804010587 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 399804010588 motif II; other site 399804010589 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 399804010590 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 399804010591 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 399804010592 active site 399804010593 Zn binding site [ion binding]; other site 399804010594 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 399804010595 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 399804010596 active site 399804010597 nucleophile elbow; other site 399804010598 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 399804010599 Surface antigen; Region: Bac_surface_Ag; pfam01103 399804010600 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 399804010601 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 399804010602 PAS fold; Region: PAS_3; pfam08447 399804010603 heme pocket [chemical binding]; other site 399804010604 putative active site [active] 399804010605 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 399804010606 PAS domain; Region: PAS_9; pfam13426 399804010607 putative active site [active] 399804010608 heme pocket [chemical binding]; other site 399804010609 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010610 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010611 metal binding site [ion binding]; metal-binding site 399804010612 active site 399804010613 I-site; other site 399804010614 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 399804010615 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 399804010616 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 399804010617 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 399804010618 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 399804010619 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 399804010620 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 399804010621 E3 interaction surface; other site 399804010622 lipoyl attachment site [posttranslational modification]; other site 399804010623 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 399804010624 E3 interaction surface; other site 399804010625 lipoyl attachment site [posttranslational modification]; other site 399804010626 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 399804010627 E3 interaction surface; other site 399804010628 lipoyl attachment site [posttranslational modification]; other site 399804010629 e3 binding domain; Region: E3_binding; pfam02817 399804010630 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 399804010631 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 399804010632 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 399804010633 dimer interface [polypeptide binding]; other site 399804010634 TPP-binding site [chemical binding]; other site 399804010635 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 399804010636 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804010637 DNA-binding site [nucleotide binding]; DNA binding site 399804010638 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 399804010639 regulatory protein AmpE; Provisional; Region: PRK10987 399804010640 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 399804010641 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 399804010642 amidase catalytic site [active] 399804010643 Zn binding residues [ion binding]; other site 399804010644 substrate binding site [chemical binding]; other site 399804010645 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 399804010646 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 399804010647 dimerization interface [polypeptide binding]; other site 399804010648 active site 399804010649 putative major pilin subunit; Provisional; Region: PRK10574 399804010650 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 399804010651 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 399804010652 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 399804010653 Walker A motif; other site 399804010654 ATP binding site [chemical binding]; other site 399804010655 Walker B motif; other site 399804010656 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 399804010657 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 399804010658 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 399804010659 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 399804010660 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 399804010661 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 399804010662 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 399804010663 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 399804010664 CoA-binding site [chemical binding]; other site 399804010665 ATP-binding [chemical binding]; other site 399804010666 hypothetical protein; Provisional; Region: PRK05287 399804010667 Domain of unknown function (DUF329); Region: DUF329; pfam03884 399804010668 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 399804010669 active site 399804010670 8-oxo-dGMP binding site [chemical binding]; other site 399804010671 nudix motif; other site 399804010672 metal binding site [ion binding]; metal-binding site 399804010673 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 399804010674 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 399804010675 catalytic residues [active] 399804010676 exopolyphosphatase; Region: exo_poly_only; TIGR03706 399804010677 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 399804010678 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 399804010679 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 399804010680 ATP binding site [chemical binding]; other site 399804010681 Mg++ binding site [ion binding]; other site 399804010682 motif III; other site 399804010683 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 399804010684 nucleotide binding region [chemical binding]; other site 399804010685 ATP-binding site [chemical binding]; other site 399804010686 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 399804010687 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 399804010688 catalytic residues [active] 399804010689 transcription termination factor Rho; Provisional; Region: rho; PRK09376 399804010690 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 399804010691 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 399804010692 RNA binding site [nucleotide binding]; other site 399804010693 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 399804010694 multimer interface [polypeptide binding]; other site 399804010695 Walker A motif; other site 399804010696 ATP binding site [chemical binding]; other site 399804010697 Walker B motif; other site 399804010698 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804010699 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804010700 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 399804010701 putative effector binding pocket; other site 399804010702 dimerization interface [polypeptide binding]; other site 399804010703 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 399804010704 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 399804010705 putative NAD(P) binding site [chemical binding]; other site 399804010706 dimer interface [polypeptide binding]; other site 399804010707 Uncharacterized conserved protein [Function unknown]; Region: COG1359 399804010708 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 399804010709 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 399804010710 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 399804010711 L-aspartate oxidase; Provisional; Region: PRK06175 399804010712 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 399804010713 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; 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:quinone...; Region: QFR_TypeB_TM; cd00581 399804010714 Iron-sulfur protein interface; other site 399804010715 proximal heme binding site [chemical binding]; other site 399804010716 distal heme binding site [chemical binding]; other site 399804010717 dimer interface [polypeptide binding]; other site 399804010718 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13554 399804010719 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; 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:quinone...; Region: QFR_TypeB_TM; cd00581 399804010720 Iron-sulfur protein interface; other site 399804010721 proximal heme binding site [chemical binding]; other site 399804010722 distal heme binding site [chemical binding]; other site 399804010723 dimer interface [polypeptide binding]; other site 399804010724 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 399804010725 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 399804010726 S-adenosylmethionine binding site [chemical binding]; other site 399804010727 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 399804010728 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 399804010729 FMN binding site [chemical binding]; other site 399804010730 active site 399804010731 catalytic residues [active] 399804010732 substrate binding site [chemical binding]; other site 399804010733 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 399804010734 global DNA-binding transcriptional dual regulator Fis; Provisional; Region: fis; PRK00430 399804010735 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 399804010736 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 399804010737 Hemerythrin-like domain; Region: Hr-like; cd12108 399804010738 Divergent AAA domain; Region: AAA_4; pfam04326 399804010739 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 399804010740 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 399804010741 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 399804010742 motif II; other site 399804010743 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 399804010744 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 399804010745 active site 399804010746 Int/Topo IB signature motif; other site 399804010747 Protein of unknown function, DUF484; Region: DUF484; cl17449 399804010748 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 399804010749 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 399804010750 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 399804010751 diaminopimelate decarboxylase; Region: lysA; TIGR01048 399804010752 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 399804010753 active site 399804010754 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 399804010755 substrate binding site [chemical binding]; other site 399804010756 catalytic residues [active] 399804010757 dimer interface [polypeptide binding]; other site 399804010758 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 399804010759 putative iron binding site [ion binding]; other site 399804010760 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 399804010761 adenylate cyclase; Provisional; Region: cyaA; PRK09450 399804010762 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 399804010763 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 399804010764 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 399804010765 domain interfaces; other site 399804010766 active site 399804010767 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 399804010768 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 399804010769 active site 399804010770 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 399804010771 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 399804010772 HemY protein N-terminus; Region: HemY_N; pfam07219 399804010773 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 399804010774 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 399804010775 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 399804010776 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 399804010777 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 399804010778 Walker A/P-loop; other site 399804010779 ATP binding site [chemical binding]; other site 399804010780 Q-loop/lid; other site 399804010781 ABC transporter signature motif; other site 399804010782 Walker B; other site 399804010783 D-loop; other site 399804010784 H-loop/switch region; other site 399804010785 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 399804010786 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804010787 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804010788 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 399804010789 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 399804010790 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 399804010791 ligand binding site [chemical binding]; other site 399804010792 Predicted transglutaminase-like cysteine proteinase [General function prediction only]; Region: COG3672 399804010793 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 399804010794 dimerization interface [polypeptide binding]; other site 399804010795 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010796 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010797 metal binding site [ion binding]; metal-binding site 399804010798 active site 399804010799 I-site; other site 399804010800 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 399804010801 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 399804010802 GAF domain; Region: GAF; pfam01590 399804010803 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 399804010804 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 399804010805 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010806 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010807 metal binding site [ion binding]; metal-binding site 399804010808 active site 399804010809 I-site; other site 399804010810 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 399804010811 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 399804010812 Part of AAA domain; Region: AAA_19; pfam13245 399804010813 Family description; Region: UvrD_C_2; pfam13538 399804010814 Membrane fusogenic activity; Region: BMFP; pfam04380 399804010815 NnrS protein; Region: NnrS; pfam05940 399804010816 Cytochrome c552; Region: Cytochrom_C552; pfam02335 399804010817 inner membrane protein; Provisional; Region: PRK11715 399804010818 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 399804010819 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 399804010820 active site 399804010821 Tim44-like domain; Region: Tim44; pfam04280 399804010822 Domain of unknown function (DUF4303); Region: DUF4303; pfam14136 399804010823 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 399804010824 homodimer interface [polypeptide binding]; other site 399804010825 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804010826 catalytic residue [active] 399804010827 threonine dehydratase; Reviewed; Region: PRK09224 399804010828 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 399804010829 tetramer interface [polypeptide binding]; other site 399804010830 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804010831 catalytic residue [active] 399804010832 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 399804010833 putative Ile/Val binding site [chemical binding]; other site 399804010834 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 399804010835 putative Ile/Val binding site [chemical binding]; other site 399804010836 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 399804010837 acetolactate synthase 2 regulatory subunit; Provisional; Region: ilvM; PRK11152 399804010838 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 399804010839 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 399804010840 PYR/PP interface [polypeptide binding]; other site 399804010841 dimer interface [polypeptide binding]; other site 399804010842 TPP binding site [chemical binding]; other site 399804010843 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 399804010844 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 399804010845 TPP-binding site [chemical binding]; other site 399804010846 dimer interface [polypeptide binding]; other site 399804010847 ketol-acid reductoisomerase; Validated; Region: PRK05225 399804010848 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 399804010849 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 399804010850 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 399804010851 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804010852 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 399804010853 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 399804010854 putative dimerization interface [polypeptide binding]; other site 399804010855 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 399804010856 Domain of unknown function DUF21; Region: DUF21; pfam01595 399804010857 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 399804010858 Transporter associated domain; Region: CorC_HlyC; smart01091 399804010859 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 399804010860 ERCC4 domain; Region: ERCC4; smart00891 399804010861 dUMP phosphatase; Provisional; Region: PRK09449 399804010862 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 399804010863 motif II; other site 399804010864 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804010865 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804010866 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 399804010867 putative effector binding pocket; other site 399804010868 dimerization interface [polypeptide binding]; other site 399804010869 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b1; cd09203 399804010870 PLD-like domain; Region: PLDc_2; pfam13091 399804010871 putative homodimer interface [polypeptide binding]; other site 399804010872 putative active site [active] 399804010873 catalytic site [active] 399804010874 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 399804010875 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 399804010876 ATP binding site [chemical binding]; other site 399804010877 putative Mg++ binding site [ion binding]; other site 399804010878 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 399804010879 nucleotide binding region [chemical binding]; other site 399804010880 ATP-binding site [chemical binding]; other site 399804010881 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 399804010882 Fic family protein [Function unknown]; Region: COG3177 399804010883 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 399804010884 Fic/DOC family; Region: Fic; pfam02661 399804010885 Sulfotransferase family; Region: Sulfotransfer_3; pfam13469 399804010886 Phosphotransferase enzyme family; Region: APH; pfam01636 399804010887 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 399804010888 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 399804010889 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 399804010890 active site 399804010891 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 399804010892 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 399804010893 catalytic site [active] 399804010894 G-X2-G-X-G-K; other site 399804010895 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 399804010896 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 399804010897 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804010898 Zn2+ binding site [ion binding]; other site 399804010899 Mg2+ binding site [ion binding]; other site 399804010900 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 399804010901 synthetase active site [active] 399804010902 NTP binding site [chemical binding]; other site 399804010903 metal binding site [ion binding]; metal-binding site 399804010904 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 399804010905 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 399804010906 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 399804010907 homotrimer interaction site [polypeptide binding]; other site 399804010908 putative active site [active] 399804010909 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 399804010910 Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase; Region: LC_FACS_bac; cd05932 399804010911 acyl-activating enzyme (AAE) consensus motif; other site 399804010912 putative AMP binding site [chemical binding]; other site 399804010913 putative active site [active] 399804010914 putative CoA binding site [chemical binding]; other site 399804010915 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 399804010916 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 399804010917 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 399804010918 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 399804010919 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 399804010920 N-terminal plug; other site 399804010921 ligand-binding site [chemical binding]; other site 399804010922 Domain of unknown function (DUF1963); Region: DUF1963; cl01600 399804010923 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 399804010924 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 399804010925 E-class dimer interface [polypeptide binding]; other site 399804010926 P-class dimer interface [polypeptide binding]; other site 399804010927 active site 399804010928 Cu2+ binding site [ion binding]; other site 399804010929 Zn2+ binding site [ion binding]; other site 399804010930 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 399804010931 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 399804010932 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 399804010933 Walker A motif; other site 399804010934 ATP binding site [chemical binding]; other site 399804010935 Walker B motif; other site 399804010936 arginine finger; other site 399804010937 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 399804010938 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 399804010939 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 399804010940 putative acyl-acceptor binding pocket; other site 399804010941 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 399804010942 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 399804010943 putative acyl-acceptor binding pocket; other site 399804010944 Uncharacterized conserved protein [Function unknown]; Region: COG1683 399804010945 Transcriptional regulators [Transcription]; Region: GntR; COG1802 399804010946 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804010947 DNA-binding site [nucleotide binding]; DNA binding site 399804010948 FCD domain; Region: FCD; pfam07729 399804010949 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 399804010950 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 399804010951 tetramer interface [polypeptide binding]; other site 399804010952 active site 399804010953 Mg2+/Mn2+ binding site [ion binding]; other site 399804010954 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 399804010955 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 399804010956 dimer interface [polypeptide binding]; other site 399804010957 active site 399804010958 citrylCoA binding site [chemical binding]; other site 399804010959 oxalacetate/citrate binding site [chemical binding]; other site 399804010960 coenzyme A binding site [chemical binding]; other site 399804010961 catalytic triad [active] 399804010962 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 399804010963 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 399804010964 substrate binding site [chemical binding]; other site 399804010965 ligand binding site [chemical binding]; other site 399804010966 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 399804010967 substrate binding site [chemical binding]; other site 399804010968 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 399804010969 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 399804010970 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 399804010971 PAS fold; Region: PAS_3; pfam08447 399804010972 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 399804010973 PAS domain; Region: PAS_9; pfam13426 399804010974 putative active site [active] 399804010975 heme pocket [chemical binding]; other site 399804010976 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804010977 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804010978 metal binding site [ion binding]; metal-binding site 399804010979 active site 399804010980 I-site; other site 399804010981 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 399804010982 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 399804010983 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 399804010984 homodimer interface [polypeptide binding]; other site 399804010985 substrate-cofactor binding pocket; other site 399804010986 catalytic residue [active] 399804010987 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; pfam07073 399804010988 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 399804010989 homotrimer interaction site [polypeptide binding]; other site 399804010990 putative active site [active] 399804010991 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 399804010992 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 399804010993 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 399804010994 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 399804010995 catalytic residues [active] 399804010996 hinge region; other site 399804010997 alpha helical domain; other site 399804010998 serine/threonine protein kinase; Provisional; Region: PRK11768 399804010999 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 399804011000 Protein of unknown function (DUF3630); Region: DUF3630; pfam12305 399804011001 Uncharacterized conserved protein [Function unknown]; Region: COG0397 399804011002 hypothetical protein; Validated; Region: PRK00029 399804011003 ribonuclease E; Reviewed; Region: rne; PRK10811 399804011004 DsrE/DsrF-like family; Region: DrsE; cl00672 399804011005 Nitrous oxide-stimulated promoter; Region: YgbA_NO; pfam11756 399804011006 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 399804011007 ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CeuA; COG4607 399804011008 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 399804011009 putative ligand binding residues [chemical binding]; other site 399804011010 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 399804011011 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 399804011012 Walker A/P-loop; other site 399804011013 ATP binding site [chemical binding]; other site 399804011014 Q-loop/lid; other site 399804011015 ABC transporter signature motif; other site 399804011016 Walker B; other site 399804011017 D-loop; other site 399804011018 H-loop/switch region; other site 399804011019 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 399804011020 ABC-ATPase subunit interface; other site 399804011021 dimer interface [polypeptide binding]; other site 399804011022 putative PBP binding regions; other site 399804011023 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 399804011024 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 399804011025 ABC-ATPase subunit interface; other site 399804011026 dimer interface [polypeptide binding]; other site 399804011027 putative PBP binding regions; other site 399804011028 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 399804011029 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 399804011030 N-terminal plug; other site 399804011031 ligand-binding site [chemical binding]; other site 399804011032 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 399804011033 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 399804011034 Walker A/P-loop; other site 399804011035 ATP binding site [chemical binding]; other site 399804011036 Q-loop/lid; other site 399804011037 ABC transporter signature motif; other site 399804011038 Walker B; other site 399804011039 D-loop; other site 399804011040 H-loop/switch region; other site 399804011041 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804011042 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 399804011043 Walker A/P-loop; other site 399804011044 ATP binding site [chemical binding]; other site 399804011045 Q-loop/lid; other site 399804011046 ABC transporter signature motif; other site 399804011047 Walker B; other site 399804011048 D-loop; other site 399804011049 H-loop/switch region; other site 399804011050 Acyltransferase family; Region: Acyl_transf_3; pfam01757 399804011051 Putative phage tail protein; Region: Phage-tail_3; pfam13550 399804011052 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 399804011053 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 399804011054 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; pfam10124 399804011055 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 399804011056 Phage virion morphogenesis family; Region: Phage_tail_S; pfam05069 399804011057 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 399804011058 Protein of unknown function (DUF935); Region: DUF935; pfam06074 399804011059 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 399804011060 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 399804011061 Terminase-like family; Region: Terminase_6; pfam03237 399804011062 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 399804011063 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 399804011064 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 399804011065 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 399804011066 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 399804011067 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 399804011068 catalytic residue [active] 399804011069 Mor transcription activator family; Region: Mor; pfam08765 399804011070 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 399804011071 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 399804011072 Uncharacterized ATPase, putative transposase [General function prediction only]; Region: COG2842 399804011073 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 399804011074 non-specific DNA binding site [nucleotide binding]; other site 399804011075 salt bridge; other site 399804011076 sequence-specific DNA binding site [nucleotide binding]; other site 399804011077 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 399804011078 Walker A motif; other site 399804011079 ATP binding site [chemical binding]; other site 399804011080 Walker B motif; other site 399804011081 Mu B transposition protein, C terminal; Region: Phage-MuB_C; pfam09077 399804011082 arginine finger; other site 399804011083 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 399804011084 Mu DNA binding, I gamma subdomain; Region: HTH_Tnp_Mu_2; pfam09039 399804011085 Bacteriophage Mu transposase; Region: DDE_2; pfam02914 399804011086 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 399804011087 Helix-turn-helix domain; Region: HTH_17; cl17695 399804011088 Winged helix-turn-helix DNA-binding; Region: HTH_35; cl17423 399804011089 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 399804011090 sequence-specific DNA binding site [nucleotide binding]; other site 399804011091 salt bridge; other site 399804011092 Predicted transcriptional regulator [Transcription]; Region: COG2932 399804011093 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 399804011094 Catalytic site [active] 399804011095 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 399804011096 multiple promoter invertase; Provisional; Region: mpi; PRK13413 399804011097 catalytic residues [active] 399804011098 catalytic nucleophile [active] 399804011099 Presynaptic Site I dimer interface [polypeptide binding]; other site 399804011100 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 399804011101 Synaptic Flat tetramer interface [polypeptide binding]; other site 399804011102 Synaptic Site I dimer interface [polypeptide binding]; other site 399804011103 DNA binding site [nucleotide binding] 399804011104 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 399804011105 DNA-binding interface [nucleotide binding]; DNA binding site 399804011106 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 399804011107 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 399804011108 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 399804011109 TIR domain; Region: TIR_2; pfam13676 399804011110 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 399804011111 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; cl01912 399804011112 Competence protein CoiA-like family; Region: CoiA; cl11541 399804011113 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 399804011114 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 399804011115 catalytic residues [active] 399804011116 catalytic nucleophile [active] 399804011117 Presynaptic Site I dimer interface [polypeptide binding]; other site 399804011118 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 399804011119 Synaptic Flat tetramer interface [polypeptide binding]; other site 399804011120 Synaptic Site I dimer interface [polypeptide binding]; other site 399804011121 DNA binding site [nucleotide binding] 399804011122 Helix-turn-helix domain of resolvase; Region: HTH_7; pfam02796 399804011123 DNA-binding interface [nucleotide binding]; DNA binding site 399804011124 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 399804011125 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804011126 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 399804011127 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804011128 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804011129 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804011130 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804011131 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 399804011132 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 399804011133 Walker A motif; other site 399804011134 ATP binding site [chemical binding]; other site 399804011135 Walker B motif; other site 399804011136 Integrase core domain; Region: rve; pfam00665 399804011137 multiple promoter invertase; Provisional; Region: mpi; PRK13413 399804011138 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 399804011139 catalytic residues [active] 399804011140 catalytic nucleophile [active] 399804011141 Presynaptic Site I dimer interface [polypeptide binding]; other site 399804011142 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 399804011143 Synaptic Flat tetramer interface [polypeptide binding]; other site 399804011144 Synaptic Site I dimer interface [polypeptide binding]; other site 399804011145 DNA binding site [nucleotide binding] 399804011146 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 399804011147 DNA-binding interface [nucleotide binding]; DNA binding site 399804011148 putative mercuric reductase; Provisional; Region: PRK13748 399804011149 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 399804011150 metal-binding site [ion binding] 399804011151 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 399804011152 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 399804011153 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 399804011154 metal-binding site [ion binding] 399804011155 MerT mercuric transport protein; Region: MerT; pfam02411 399804011156 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 399804011157 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 399804011158 DNA binding residues [nucleotide binding] 399804011159 dimer interface [polypeptide binding]; other site 399804011160 mercury binding site [ion binding]; other site 399804011161 DNA-specific endonuclease I; Provisional; Region: PRK15137 399804011162 Endonuclease I; Region: Endonuclease_1; pfam04231 399804011163 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 399804011164 active site 399804011165 DNA binding site [nucleotide binding] 399804011166 Int/Topo IB signature motif; other site 399804011167 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 399804011168 DNA-binding site [nucleotide binding]; DNA binding site 399804011169 RNA-binding motif; other site 399804011170 Putative helicase; Region: TraI_2; pfam07514 399804011171 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 399804011172 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 399804011173 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 399804011174 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 399804011175 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 399804011176 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 399804011177 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 399804011178 Restriction endonuclease; Region: Mrr_cat; pfam04471 399804011179 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804011180 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804011181 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 399804011182 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804011183 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 399804011184 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804011185 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804011186 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 399804011187 generic binding surface II; other site 399804011188 generic binding surface I; other site 399804011189 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 399804011190 Uncharacterized protein family UPF0547; Region: UPF0547; pfam10571 399804011191 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804011192 Coenzyme A binding pocket [chemical binding]; other site 399804011193 PilZ domain; Region: PilZ; pfam07238 399804011194 hypothetical protein; Provisional; Region: PRK09272 399804011195 Penicillinase repressor; Region: Pencillinase_R; cl17580 399804011196 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]; Region: MecR1; COG4219 399804011197 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 399804011198 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 399804011199 E3 interaction surface; other site 399804011200 lipoyl attachment site [posttranslational modification]; other site 399804011201 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804011202 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 399804011203 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 399804011204 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 399804011205 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 399804011206 non-specific DNA binding site [nucleotide binding]; other site 399804011207 salt bridge; other site 399804011208 sequence-specific DNA binding site [nucleotide binding]; other site 399804011209 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 399804011210 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; cl17880 399804011211 heme exporter protein CcmC; Region: ccmC; TIGR01191 399804011212 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 399804011213 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 399804011214 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 399804011215 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 399804011216 putative C-terminal domain interface [polypeptide binding]; other site 399804011217 putative GSH binding site (G-site) [chemical binding]; other site 399804011218 putative dimer interface [polypeptide binding]; other site 399804011219 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 399804011220 N-terminal domain interface [polypeptide binding]; other site 399804011221 dimer interface [polypeptide binding]; other site 399804011222 substrate binding pocket (H-site) [chemical binding]; other site 399804011223 Transposase domain (DUF772); Region: DUF772; pfam05598 399804011224 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 399804011225 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804011226 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804011227 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804011228 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804011229 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804011230 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 399804011231 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 399804011232 FtsX-like permease family; Region: FtsX; pfam02687 399804011233 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 399804011234 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 399804011235 Walker A/P-loop; other site 399804011236 ATP binding site [chemical binding]; other site 399804011237 Q-loop/lid; other site 399804011238 ABC transporter signature motif; other site 399804011239 Walker B; other site 399804011240 D-loop; other site 399804011241 H-loop/switch region; other site 399804011242 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 399804011243 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804011244 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 399804011245 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 399804011246 dimer interface [polypeptide binding]; other site 399804011247 active site 399804011248 metal binding site [ion binding]; metal-binding site 399804011249 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 399804011250 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 399804011251 NAD(P) binding site [chemical binding]; other site 399804011252 catalytic residues [active] 399804011253 Phospholipid methyltransferase; Region: PEMT; pfam04191 399804011254 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 399804011255 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 399804011256 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 399804011257 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 399804011258 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 399804011259 cofactor binding site; other site 399804011260 DNA binding site [nucleotide binding] 399804011261 substrate interaction site [chemical binding]; other site 399804011262 Protein of unknown function (DUF3590); Region: DUF3590; pfam12148 399804011263 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 399804011264 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 399804011265 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 399804011266 Magnesium ion binding site [ion binding]; other site 399804011267 AAA domain; Region: AAA_25; pfam13481 399804011268 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 399804011269 Walker A motif; other site 399804011270 ATP binding site [chemical binding]; other site 399804011271 Walker B motif; other site 399804011272 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 399804011273 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 399804011274 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 399804011275 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 399804011276 Walker A motif; other site 399804011277 ATP binding site [chemical binding]; other site 399804011278 Walker B motif; other site 399804011279 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 399804011280 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 399804011281 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 399804011282 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 399804011283 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 399804011284 active site 399804011285 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 399804011286 Protein of unknown function (DUF2976); Region: DUF2976; pfam11190 399804011287 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 399804011288 Protein of unknown function (DUF2895); Region: DUF2895; pfam11444 399804011289 Protein of unknown function (DUF3438); Region: DUF3438; cl13372 399804011290 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 399804011291 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 399804011292 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 399804011293 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 399804011294 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 399804011295 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 399804011296 TraU protein; Region: TraU; pfam06834 399804011297 H-NS histone family; Region: Histone_HNS; pfam00816 399804011298 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 399804011299 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 399804011300 non-specific DNA binding site [nucleotide binding]; other site 399804011301 salt bridge; other site 399804011302 sequence-specific DNA binding site [nucleotide binding]; other site 399804011303 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 399804011304 active site 399804011305 catalytic residues [active] 399804011306 DNA binding site [nucleotide binding] 399804011307 Int/Topo IB signature motif; other site 399804011308 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 399804011309 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 399804011310 non-specific DNA binding site [nucleotide binding]; other site 399804011311 salt bridge; other site 399804011312 sequence-specific DNA binding site [nucleotide binding]; other site 399804011313 Domain of unknown function (DUF955); Region: DUF955; cl01076 399804011314 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 399804011315 HsdM N-terminal domain; Region: HsdM_N; pfam12161 399804011316 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 399804011317 S-adenosylmethionine binding site [chemical binding]; other site 399804011318 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 399804011319 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 399804011320 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 399804011321 Fic family protein [Function unknown]; Region: COG3177 399804011322 Fic/DOC family; Region: Fic; pfam02661 399804011323 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 399804011324 non-specific DNA interactions [nucleotide binding]; other site 399804011325 DNA binding site [nucleotide binding] 399804011326 sequence specific DNA binding site [nucleotide binding]; other site 399804011327 putative cAMP binding site [chemical binding]; other site 399804011328 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 399804011329 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 399804011330 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 399804011331 ATP binding site [chemical binding]; other site 399804011332 putative Mg++ binding site [ion binding]; other site 399804011333 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 399804011334 Catalytic site [active] 399804011335 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 399804011336 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 399804011337 active site 399804011338 DNA binding site [nucleotide binding] 399804011339 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 399804011340 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 399804011341 Ribosome modulation factor; Region: RMF; cl01207 399804011342 RecT family; Region: RecT; cl04285 399804011343 DNA topoisomerase III; Provisional; Region: PRK07726 399804011344 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 399804011345 active site 399804011346 putative interdomain interaction site [polypeptide binding]; other site 399804011347 putative metal-binding site [ion binding]; other site 399804011348 putative nucleotide binding site [chemical binding]; other site 399804011349 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; cl11986 399804011350 domain I; other site 399804011351 DNA binding groove [nucleotide binding] 399804011352 phosphate binding site [ion binding]; other site 399804011353 domain II; other site 399804011354 domain III; other site 399804011355 nucleotide binding site [chemical binding]; other site 399804011356 catalytic site [active] 399804011357 domain IV; other site 399804011358 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 399804011359 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 399804011360 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 399804011361 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 399804011362 Walker A motif; other site 399804011363 ATP binding site [chemical binding]; other site 399804011364 Walker B motif; other site 399804011365 Protein of unknown function (DUF3150); Region: DUF3150; pfam11348 399804011366 metal ion transporter CorA-like divalent cation transporter superfamily; Region: MIT_CorA-like; cl00459 399804011367 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 399804011368 metal ion-dependent adhesion site (MIDAS); other site 399804011369 CHC2 zinc finger; Region: zf-CHC2; cl17510 399804011370 Toprim domain; Region: Toprim_3; pfam13362 399804011371 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 399804011372 active site 399804011373 Int/Topo IB signature motif; other site 399804011374 catalytic residues [active] 399804011375 DNA binding site [nucleotide binding] 399804011376 Abi-like protein; Region: Abi_2; cl01988 399804011377 hypothetical protein; Provisional; Region: PRK02237 399804011378 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 399804011379 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 399804011380 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 399804011381 DNA binding residues [nucleotide binding] 399804011382 dimer interface [polypeptide binding]; other site 399804011383 putative metal binding site [ion binding]; other site 399804011384 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 399804011385 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 399804011386 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 399804011387 carboxyltransferase (CT) interaction site; other site 399804011388 biotinylation site [posttranslational modification]; other site 399804011389 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804011390 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 399804011391 Protein of unknown function (DUF3703); Region: DUF3703; pfam12487 399804011392 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 399804011393 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 399804011394 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 399804011395 subunit interaction site [polypeptide binding]; other site 399804011396 PHB binding site; other site 399804011397 CoenzymeA binding site [chemical binding]; other site 399804011398 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 399804011399 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 399804011400 CoenzymeA binding site [chemical binding]; other site 399804011401 subunit interaction site [polypeptide binding]; other site 399804011402 PHB binding site; other site 399804011403 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 399804011404 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 399804011405 active site 399804011406 catalytic tetrad [active] 399804011407 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804011408 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804011409 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 399804011410 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 399804011411 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 399804011412 putative C-terminal domain interface [polypeptide binding]; other site 399804011413 putative GSH binding site (G-site) [chemical binding]; other site 399804011414 putative dimer interface [polypeptide binding]; other site 399804011415 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 399804011416 N-terminal domain interface [polypeptide binding]; other site 399804011417 dimer interface [polypeptide binding]; other site 399804011418 substrate binding pocket (H-site) [chemical binding]; other site 399804011419 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 399804011420 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 399804011421 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 399804011422 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 399804011423 active site 399804011424 catalytic residues [active] 399804011425 DNA binding site [nucleotide binding] 399804011426 Int/Topo IB signature motif; other site 399804011427 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 399804011428 non-specific DNA binding site [nucleotide binding]; other site 399804011429 salt bridge; other site 399804011430 sequence-specific DNA binding site [nucleotide binding]; other site 399804011431 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 399804011432 Putative phage tail protein; Region: Phage-tail_3; pfam13550 399804011433 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 399804011434 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 399804011435 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; pfam10124 399804011436 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 399804011437 Phage virion morphogenesis family; Region: Phage_tail_S; pfam05069 399804011438 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 399804011439 Protein of unknown function (DUF935); Region: DUF935; pfam06074 399804011440 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 399804011441 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 399804011442 Terminase-like family; Region: Terminase_6; pfam03237 399804011443 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 399804011444 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 399804011445 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 399804011446 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 399804011447 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 399804011448 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 399804011449 catalytic residue [active] 399804011450 Mor transcription activator family; Region: Mor; pfam08765 399804011451 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 399804011452 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 399804011453 Uncharacterized ATPase, putative transposase [General function prediction only]; Region: COG2842 399804011454 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 399804011455 non-specific DNA binding site [nucleotide binding]; other site 399804011456 salt bridge; other site 399804011457 sequence-specific DNA binding site [nucleotide binding]; other site 399804011458 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 399804011459 Walker A motif; other site 399804011460 ATP binding site [chemical binding]; other site 399804011461 Walker B motif; other site 399804011462 Mu B transposition protein, C terminal; Region: Phage-MuB_C; pfam09077 399804011463 arginine finger; other site 399804011464 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 399804011465 Mu DNA binding, I gamma subdomain; Region: HTH_Tnp_Mu_2; pfam09039 399804011466 Bacteriophage Mu transposase; Region: DDE_2; pfam02914 399804011467 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 399804011468 Helix-turn-helix domain; Region: HTH_17; cl17695 399804011469 Winged helix-turn-helix DNA-binding; Region: HTH_35; cl17423 399804011470 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 399804011471 sequence-specific DNA binding site [nucleotide binding]; other site 399804011472 salt bridge; other site 399804011473 Predicted transcriptional regulator [Transcription]; Region: COG2932 399804011474 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 399804011475 Catalytic site [active] 399804011476 Uncharacterized conserved protein [Function unknown]; Region: COG3339 399804011477 ornithine decarboxylase; Provisional; Region: PRK13578 399804011478 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 399804011479 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 399804011480 homodimer interface [polypeptide binding]; other site 399804011481 pyridoxal 5'-phosphate binding site [chemical binding]; other site 399804011482 catalytic residue [active] 399804011483 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 399804011484 putrescine transporter; Provisional; Region: potE; PRK10655 399804011485 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 399804011486 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 399804011487 trimer interface [polypeptide binding]; other site 399804011488 eyelet of channel; other site 399804011489 hypothetical protein; Provisional; Region: PRK01254 399804011490 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 399804011491 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 399804011492 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 399804011493 MAPEG family; Region: MAPEG; cl09190 399804011494 Uncharacterized conserved protein [Function unknown]; Region: COG2966 399804011495 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 399804011496 Uncharacterized conserved protein [Function unknown]; Region: COG3610 399804011497 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 399804011498 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 399804011499 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 399804011500 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 399804011501 conserved cys residue [active] 399804011502 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804011503 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804011504 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 399804011505 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 399804011506 putative SAM binding site [chemical binding]; other site 399804011507 putative homodimer interface [polypeptide binding]; other site 399804011508 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 399804011509 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 399804011510 putative ligand binding site [chemical binding]; other site 399804011511 hypothetical protein; Reviewed; Region: PRK12497 399804011512 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 399804011513 dimer interface [polypeptide binding]; other site 399804011514 active site 399804011515 BON domain; Region: BON; pfam04972 399804011516 BON domain; Region: BON; pfam04972 399804011517 EamA-like transporter family; Region: EamA; pfam00892 399804011518 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 399804011519 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 399804011520 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804011521 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 399804011522 dimerization interface [polypeptide binding]; other site 399804011523 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 399804011524 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 399804011525 active site 399804011526 HIGH motif; other site 399804011527 dimer interface [polypeptide binding]; other site 399804011528 KMSKS motif; other site 399804011529 phosphoglycolate phosphatase; Provisional; Region: PRK13222 399804011530 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 399804011531 motif II; other site 399804011532 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 399804011533 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 399804011534 substrate binding site [chemical binding]; other site 399804011535 hexamer interface [polypeptide binding]; other site 399804011536 metal binding site [ion binding]; metal-binding site 399804011537 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 399804011538 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 399804011539 AAA ATPase domain; Region: AAA_16; pfam13191 399804011540 AAA domain; Region: AAA_22; pfam13401 399804011541 Walker A motif; other site 399804011542 ATP binding site [chemical binding]; other site 399804011543 Walker B motif; other site 399804011544 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 399804011545 active site 399804011546 dimer interface [polypeptide binding]; other site 399804011547 metal binding site [ion binding]; metal-binding site 399804011548 shikimate kinase; Reviewed; Region: aroK; PRK00131 399804011549 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 399804011550 ADP binding site [chemical binding]; other site 399804011551 magnesium binding site [ion binding]; other site 399804011552 putative shikimate binding site; other site 399804011553 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 399804011554 Secretin and TonB N terminus short domain; Region: STN; smart00965 399804011555 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 399804011556 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 399804011557 Pilus assembly protein, PilP; Region: PilP; pfam04351 399804011558 Pilus assembly protein, PilO; Region: PilO; pfam04350 399804011559 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 399804011560 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 399804011561 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 399804011562 Competence protein A; Region: Competence_A; pfam11104 399804011563 nucleotide binding site [chemical binding]; other site 399804011564 Cell division protein FtsA; Region: FtsA; pfam14450 399804011565 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 399804011566 Transglycosylase; Region: Transgly; pfam00912 399804011567 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 399804011568 argininosuccinate lyase; Provisional; Region: PRK04833 399804011569 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 399804011570 active sites [active] 399804011571 tetramer interface [polypeptide binding]; other site 399804011572 argininosuccinate synthase; Provisional; Region: PRK13820 399804011573 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 399804011574 ANP binding site [chemical binding]; other site 399804011575 Substrate Binding Site II [chemical binding]; other site 399804011576 Substrate Binding Site I [chemical binding]; other site 399804011577 ornithine carbamoyltransferase; Provisional; Region: PRK14805 399804011578 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 399804011579 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 399804011580 acetylglutamate kinase; Provisional; Region: PRK00942 399804011581 nucleotide binding site [chemical binding]; other site 399804011582 substrate binding site [chemical binding]; other site 399804011583 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 399804011584 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 399804011585 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 399804011586 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 399804011587 Protein of unknown function (DUF1439); Region: DUF1439; pfam07273 399804011588 competence damage-inducible protein A; Provisional; Region: PRK00549 399804011589 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 399804011590 putative MPT binding site; other site 399804011591 Competence-damaged protein; Region: CinA; pfam02464 399804011592 Helix-turn-helix domain; Region: HTH_17; pfam12728 399804011593 PBP superfamily domain; Region: PBP_like; pfam12727 399804011594 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 399804011595 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 399804011596 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 399804011597 Ferredoxin [Energy production and conversion]; Region: COG1146 399804011598 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 399804011599 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 399804011600 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 399804011601 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 399804011602 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 399804011603 [4Fe-4S] binding site [ion binding]; other site 399804011604 molybdopterin cofactor binding site; other site 399804011605 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 399804011606 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 399804011607 molybdopterin cofactor binding site; other site 399804011608 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 399804011609 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 399804011610 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 399804011611 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 399804011612 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 399804011613 [4Fe-4S] binding site [ion binding]; other site 399804011614 molybdopterin cofactor binding site; other site 399804011615 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 399804011616 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 399804011617 molybdopterin cofactor binding site; other site 399804011618 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 399804011619 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 399804011620 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 399804011621 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 399804011622 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 399804011623 N-terminal plug; other site 399804011624 ligand-binding site [chemical binding]; other site 399804011625 Methyltransferase domain; Region: Methyltransf_23; pfam13489 399804011626 Methyltransferase domain; Region: Methyltransf_11; pfam08241 399804011627 PAS domain S-box; Region: sensory_box; TIGR00229 399804011628 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 399804011629 putative active site [active] 399804011630 heme pocket [chemical binding]; other site 399804011631 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804011632 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804011633 metal binding site [ion binding]; metal-binding site 399804011634 active site 399804011635 I-site; other site 399804011636 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 399804011637 DTW domain; Region: DTW; cl01221 399804011638 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 399804011639 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 399804011640 putative substrate translocation pore; other site 399804011641 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 399804011642 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804011643 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 399804011644 substrate binding pocket [chemical binding]; other site 399804011645 dimerization interface [polypeptide binding]; other site 399804011646 Cache domain; Region: Cache_1; pfam02743 399804011647 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 399804011648 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 399804011649 dimerization interface [polypeptide binding]; other site 399804011650 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 399804011651 dimer interface [polypeptide binding]; other site 399804011652 putative CheW interface [polypeptide binding]; other site 399804011653 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 399804011654 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 399804011655 Sel1-like repeats; Region: SEL1; smart00671 399804011656 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 399804011657 Protein of unknown function VcgC/VcgE (DUF2780); Region: DUF2780; pfam11075 399804011658 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 399804011659 putative metal binding site [ion binding]; other site 399804011660 Spore germination protein; Region: Spore_permease; cl17796 399804011661 putative transporter; Provisional; Region: PRK11021 399804011662 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 399804011663 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 399804011664 dimerization interface [polypeptide binding]; other site 399804011665 putative Zn2+ binding site [ion binding]; other site 399804011666 putative DNA binding site [nucleotide binding]; other site 399804011667 AsnC family; Region: AsnC_trans_reg; pfam01037 399804011668 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 399804011669 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 399804011670 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 399804011671 cytochrome c nitrite reductase pentaheme subunit; Provisional; Region: PRK11659 399804011672 Transcriptional regulator [Transcription]; Region: LysR; COG0583 399804011673 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 399804011674 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 399804011675 dimerization interface [polypeptide binding]; other site 399804011676 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 399804011677 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 399804011678 dimer interface [polypeptide binding]; other site 399804011679 tetramer interface [polypeptide binding]; other site 399804011680 PYR/PP interface [polypeptide binding]; other site 399804011681 TPP binding site [chemical binding]; other site 399804011682 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 399804011683 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 399804011684 TPP-binding site; other site 399804011685 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 399804011686 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 399804011687 nucleophilic elbow; other site 399804011688 catalytic triad; other site 399804011689 O-succinylbenzoate synthase; Provisional; Region: PRK05105 399804011690 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 399804011691 active site 399804011692 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 399804011693 O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE); Region: OSB_CoA_lg; cd05912 399804011694 acyl-activating enzyme (AAE) consensus motif; other site 399804011695 putative AMP binding site [chemical binding]; other site 399804011696 putative active site [active] 399804011697 putative CoA binding site [chemical binding]; other site 399804011698 FimV N-terminal domain; Region: FimV_core; TIGR03505 399804011699 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 399804011700 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 399804011701 active site 399804011702 phosphorylation site [posttranslational modification] 399804011703 intermolecular recognition site; other site 399804011704 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 399804011705 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 399804011706 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 399804011707 active site 399804011708 phosphorylation site [posttranslational modification] 399804011709 intermolecular recognition site; other site 399804011710 dimerization interface [polypeptide binding]; other site 399804011711 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 399804011712 DNA binding residues [nucleotide binding] 399804011713 dimerization interface [polypeptide binding]; other site 399804011714 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804011715 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804011716 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804011717 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804011718 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 399804011719 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 399804011720 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 399804011721 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 399804011722 Fimbrial protein; Region: Fimbrial; cl01416 399804011723 Fimbrial protein; Region: Fimbrial; cl01416 399804011724 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 399804011725 PapC N-terminal domain; Region: PapC_N; pfam13954 399804011726 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 399804011727 PapC C-terminal domain; Region: PapC_C; pfam13953 399804011728 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 399804011729 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 399804011730 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 399804011731 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 399804011732 Fimbrial protein; Region: Fimbrial; cl01416 399804011733 Fimbrial protein; Region: Fimbrial; cl01416 399804011734 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 399804011735 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 399804011736 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 399804011737 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 399804011738 DNA binding residues [nucleotide binding] 399804011739 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 399804011740 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 399804011741 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 399804011742 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804011743 Walker A/P-loop; other site 399804011744 ATP binding site [chemical binding]; other site 399804011745 Q-loop/lid; other site 399804011746 ABC transporter signature motif; other site 399804011747 Walker B; other site 399804011748 D-loop; other site 399804011749 H-loop/switch region; other site 399804011750 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 399804011751 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 399804011752 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 399804011753 P loop; other site 399804011754 GTP binding site [chemical binding]; other site 399804011755 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 399804011756 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 399804011757 S-adenosylmethionine binding site [chemical binding]; other site 399804011758 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 399804011759 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 399804011760 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 399804011761 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804011762 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804011763 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 399804011764 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 399804011765 active site 399804011766 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 399804011767 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 399804011768 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 399804011769 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 399804011770 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 399804011771 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 399804011772 putative active site [active] 399804011773 Zn binding site [ion binding]; other site 399804011774 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 399804011775 S-adenosylmethionine binding site [chemical binding]; other site 399804011776 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 399804011777 GIY-YIG motif/motif A; other site 399804011778 putative active site [active] 399804011779 putative metal binding site [ion binding]; other site 399804011780 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 399804011781 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 399804011782 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK03353 399804011783 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 399804011784 Nitrate and nitrite sensing; Region: NIT; pfam08376 399804011785 HAMP domain; Region: HAMP; pfam00672 399804011786 dimerization interface [polypeptide binding]; other site 399804011787 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 399804011788 PAS domain; Region: PAS_9; pfam13426 399804011789 putative active site [active] 399804011790 heme pocket [chemical binding]; other site 399804011791 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804011792 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804011793 metal binding site [ion binding]; metal-binding site 399804011794 active site 399804011795 I-site; other site 399804011796 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 399804011797 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 399804011798 Ferritin-like domain; Region: Ferritin; pfam00210 399804011799 ferroxidase diiron center [ion binding]; other site 399804011800 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 399804011801 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 399804011802 dimer interface [polypeptide binding]; other site 399804011803 putative functional site; other site 399804011804 putative MPT binding site; other site 399804011805 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 399804011806 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 399804011807 ATP binding site [chemical binding]; other site 399804011808 substrate interface [chemical binding]; other site 399804011809 Inhibitor of apoptosis-promoting Bax1; Region: Bax1-I; pfam01027 399804011810 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 399804011811 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 399804011812 S-adenosylmethionine binding site [chemical binding]; other site 399804011813 flagellar basal body-associated protein FliL-like protein; Validated; Region: PRK05697 399804011814 Chorismate lyase; Region: Chor_lyase; cl01230 399804011815 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4412 399804011816 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 399804011817 putative antibiotic transporter; Provisional; Region: PRK10739 399804011818 Glycogen synthase [Carbohydrate transport and metabolism]; Region: GlgA; COG0297 399804011819 NRDE protein; Region: NRDE; cl01315 399804011820 SnoaL-like domain; Region: SnoaL_3; pfam13474 399804011821 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 399804011822 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 399804011823 putative acyl-acceptor binding pocket; other site 399804011824 LysE type translocator; Region: LysE; cl00565 399804011825 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 399804011826 Mechanosensitive ion channel; Region: MS_channel; pfam00924 399804011827 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 399804011828 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 399804011829 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 399804011830 catalytic residues [active] 399804011831 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 399804011832 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 399804011833 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 399804011834 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 399804011835 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 399804011836 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 399804011837 DsbD alpha interface [polypeptide binding]; other site 399804011838 catalytic residues [active] 399804011839 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 399804011840 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 399804011841 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 399804011842 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 399804011843 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 399804011844 Peptidase family M48; Region: Peptidase_M48; cl12018 399804011845 Pilin (bacterial filament); Region: Pilin; pfam00114 399804011846 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 399804011847 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 399804011848 Coenzyme A binding pocket [chemical binding]; other site 399804011849 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 399804011850 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 399804011851 S-adenosylmethionine binding site [chemical binding]; other site 399804011852 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 399804011853 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804011854 metal binding site [ion binding]; metal-binding site 399804011855 active site 399804011856 I-site; other site 399804011857 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 399804011858 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 399804011859 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 399804011860 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 399804011861 N-acetyl-D-glucosamine binding site [chemical binding]; other site 399804011862 catalytic residue [active] 399804011863 LemA family; Region: LemA; cl00742 399804011864 AbgT putative transporter family; Region: ABG_transport; pfam03806 399804011865 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 399804011866 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 399804011867 Protein export membrane protein; Region: SecD_SecF; cl14618 399804011868 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 399804011869 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804011870 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804011871 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 399804011872 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 399804011873 C-terminal domain interface [polypeptide binding]; other site 399804011874 GSH binding site (G-site) [chemical binding]; other site 399804011875 dimer interface [polypeptide binding]; other site 399804011876 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 399804011877 N-terminal domain interface [polypeptide binding]; other site 399804011878 dimer interface [polypeptide binding]; other site 399804011879 substrate binding pocket (H-site) [chemical binding]; other site 399804011880 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 399804011881 active site 399804011882 oligopeptidase A; Provisional; Region: PRK10911 399804011883 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 399804011884 active site 399804011885 Zn binding site [ion binding]; other site 399804011886 Restriction endonuclease; Region: Mrr_cat; pfam04471 399804011887 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804011888 Walker A/P-loop; other site 399804011889 ATP binding site [chemical binding]; other site 399804011890 Protein of unknown function (DUF3732); Region: DUF3732; pfam12532 399804011891 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 399804011892 active site 399804011893 catalytic residues [active] 399804011894 DNA binding site [nucleotide binding] 399804011895 Int/Topo IB signature motif; other site 399804011896 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 399804011897 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 399804011898 active site 399804011899 metal binding site [ion binding]; metal-binding site 399804011900 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 399804011901 HAD superfamily (subfamily IA) hydrolase, TIGR02253; Region: CTE7 399804011902 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 399804011903 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 399804011904 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 399804011905 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804011906 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804011907 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804011908 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804011909 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 399804011910 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 399804011911 Na binding site [ion binding]; other site 399804011912 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 399804011913 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 399804011914 putative catalytic cysteine [active] 399804011915 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 399804011916 active sites [active] 399804011917 tetramer interface [polypeptide binding]; other site 399804011918 urocanate hydratase; Provisional; Region: PRK05414 399804011919 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 399804011920 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804011921 DNA-binding site [nucleotide binding]; DNA binding site 399804011922 UTRA domain; Region: UTRA; pfam07702 399804011923 imidazolonepropionase; Validated; Region: PRK09356 399804011924 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 399804011925 active site 399804011926 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 399804011927 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 399804011928 FAD binding pocket [chemical binding]; other site 399804011929 FAD binding motif [chemical binding]; other site 399804011930 phosphate binding motif [ion binding]; other site 399804011931 NAD binding pocket [chemical binding]; other site 399804011932 Transcriptional regulators [Transcription]; Region: MarR; COG1846 399804011933 MarR family; Region: MarR_2; pfam12802 399804011934 MarR family; Region: MarR_2; cl17246 399804011935 Putative phosphatase (DUF442); Region: DUF442; cl17385 399804011936 Membrane domain of glycerophosphoryl diester phosphodiesterase; Region: GPDPase_memb; pfam10110 399804011937 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 399804011938 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_memb_like; cd08579 399804011939 putative active site [active] 399804011940 catalytic site [active] 399804011941 putative metal binding site [ion binding]; other site 399804011942 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 399804011943 Uncharacterized conserved protein [Function unknown]; Region: COG3791 399804011944 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 399804011945 active site 399804011946 Predicted acetyltransferase [General function prediction only]; Region: COG2388 399804011947 HPP family; Region: HPP; pfam04982 399804011948 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 399804011949 active site 399804011950 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 399804011951 Insertion element 4 transposase N-terminal; Region: Nterm_IS4; pfam13006 399804011952 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804011953 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 399804011954 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 399804011955 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 399804011956 acyl-activating enzyme (AAE) consensus motif; other site 399804011957 putative AMP binding site [chemical binding]; other site 399804011958 putative active site [active] 399804011959 putative CoA binding site [chemical binding]; other site 399804011960 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 399804011961 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 399804011962 Walker A/P-loop; other site 399804011963 ATP binding site [chemical binding]; other site 399804011964 Q-loop/lid; other site 399804011965 ABC transporter signature motif; other site 399804011966 Walker B; other site 399804011967 D-loop; other site 399804011968 H-loop/switch region; other site 399804011969 Predicted transcriptional regulators [Transcription]; Region: COG1725 399804011970 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 399804011971 DNA-binding site [nucleotide binding]; DNA binding site 399804011972 TAP-like protein; Region: Abhydrolase_4; pfam08386 399804011973 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 399804011974 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 399804011975 Walker A/P-loop; other site 399804011976 ATP binding site [chemical binding]; other site 399804011977 Q-loop/lid; other site 399804011978 ABC transporter signature motif; other site 399804011979 Walker B; other site 399804011980 D-loop; other site 399804011981 H-loop/switch region; other site 399804011982 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 399804011983 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 399804011984 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 399804011985 MPT binding site; other site 399804011986 trimer interface [polypeptide binding]; other site 399804011987 NlpC/P60 family; Region: NLPC_P60; pfam00877 399804011988 F plasmid transfer operon, TraF, protein; Region: TraF_2; pfam13729 399804011989 Pirin-related protein [General function prediction only]; Region: COG1741 399804011990 Pirin; Region: Pirin; pfam02678 399804011991 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 399804011992 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 399804011993 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 399804011994 dimer interface [polypeptide binding]; other site 399804011995 phosphorylation site [posttranslational modification] 399804011996 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 399804011997 ATP binding site [chemical binding]; other site 399804011998 Mg2+ binding site [ion binding]; other site 399804011999 G-X-G motif; other site 399804012000 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804012001 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 399804012002 active site 399804012003 phosphorylation site [posttranslational modification] 399804012004 intermolecular recognition site; other site 399804012005 dimerization interface [polypeptide binding]; other site 399804012006 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 399804012007 DNA binding site [nucleotide binding] 399804012008 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 399804012009 TrkA-N domain; Region: TrkA_N; pfam02254 399804012010 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 399804012011 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 399804012012 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 399804012013 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 399804012014 HI0933-like protein; Region: HI0933_like; pfam03486 399804012015 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 399804012016 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 399804012017 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 399804012018 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 399804012019 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 399804012020 SecA binding site; other site 399804012021 Preprotein binding site; other site 399804012022 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 399804012023 active site residue [active] 399804012024 phosphoglyceromutase; Provisional; Region: PRK05434 399804012025 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 399804012026 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 399804012027 Peptidase family M23; Region: Peptidase_M23; pfam01551 399804012028 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 399804012029 C-terminal peptidase (prc); Region: prc; TIGR00225 399804012030 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 399804012031 protein binding site [polypeptide binding]; other site 399804012032 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 399804012033 Catalytic dyad [active] 399804012034 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 399804012035 NodB motif; other site 399804012036 putative active site [active] 399804012037 putative catalytic site [active] 399804012038 Zn binding site [ion binding]; other site 399804012039 Transcriptional regulator; Region: Rrf2; cl17282 399804012040 Rrf2 family protein; Region: rrf2_super; TIGR00738 399804012041 Flagellin N-methylase; Region: FliB; cl00497 399804012042 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 399804012043 active site 399804012044 catalytic residues [active] 399804012045 Int/Topo IB signature motif; other site 399804012046 DNA binding site [nucleotide binding] 399804012047 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 399804012048 Zn2+ binding site [ion binding]; other site 399804012049 Mg2+ binding site [ion binding]; other site 399804012050 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 399804012051 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 399804012052 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 399804012053 active site 399804012054 DNA binding site [nucleotide binding] 399804012055 Int/Topo IB signature motif; other site 399804012056 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 399804012057 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804012058 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804012059 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804012060 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 399804012061 Homeodomain-like domain; Region: HTH_23; pfam13384 399804012062 Winged helix-turn helix; Region: HTH_33; pfam13592 399804012063 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804012064 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804012065 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804012066 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804012067 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 399804012068 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 399804012069 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 399804012070 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 399804012071 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 399804012072 molybdopterin cofactor binding site; other site 399804012073 The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted...; Region: MopB_CT_DmsA-EC; cd02794 399804012074 putative molybdopterin cofactor binding site; other site 399804012075 Protein of unknown function (DUF3374); Region: DUF3374; pfam11854 399804012076 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 399804012077 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 399804012078 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 399804012079 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 399804012080 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804012081 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 399804012082 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804012083 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804012084 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804012085 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804012086 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 399804012087 Homeodomain-like domain; Region: HTH_23; pfam13384 399804012088 Winged helix-turn helix; Region: HTH_33; pfam13592 399804012089 DDE superfamily endonuclease; Region: DDE_3; pfam13358 399804012090 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 399804012091 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 399804012092 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 399804012093 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 399804012094 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 399804012095 substrate binding site [chemical binding]; other site 399804012096 oxyanion hole (OAH) forming residues; other site 399804012097 trimer interface [polypeptide binding]; other site 399804012098 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 399804012099 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 399804012100 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 399804012101 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 399804012102 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 399804012103 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 399804012104 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804012105 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 399804012106 Putative small multi-drug export protein; Region: Sm_multidrug_ex; pfam06695 399804012107 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 399804012108 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 399804012109 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 399804012110 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 399804012111 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 399804012112 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 399804012113 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 399804012114 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 399804012115 tyrosyl-tRNA synthetase; Provisional; Region: PRK13354 399804012116 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 399804012117 active site 399804012118 HIGH motif; other site 399804012119 dimer interface [polypeptide binding]; other site 399804012120 KMSKS motif; other site 399804012121 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 399804012122 RNA binding surface [nucleotide binding]; other site 399804012123 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 399804012124 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 399804012125 DNA binding residues [nucleotide binding] 399804012126 dimerization interface [polypeptide binding]; other site 399804012127 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 399804012128 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 399804012129 metal binding site [ion binding]; metal-binding site 399804012130 active site 399804012131 I-site; other site 399804012132 TniQ; Region: TniQ; pfam06527 399804012133 AAA domain; Region: AAA_22; pfam13401 399804012134 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 399804012135 Walker A motif; other site 399804012136 ATP binding site [chemical binding]; other site 399804012137 Walker B motif; other site 399804012138 Tn7 transposition regulator TnsC; Region: Tn7_TnsC_Int; pfam11426 399804012139 Integrase core domain; Region: rve; pfam00665 399804012140 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 399804012141 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 399804012142 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 399804012143 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 399804012144 glutaminase active site [active] 399804012145 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 399804012146 dimer interface [polypeptide binding]; other site 399804012147 active site 399804012148 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 399804012149 dimer interface [polypeptide binding]; other site 399804012150 active site 399804012151 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 399804012152 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 399804012153 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 399804012154 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 399804012155 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 399804012156 N-terminal plug; other site 399804012157 ligand-binding site [chemical binding]; other site 399804012158 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 399804012159 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 399804012160 Substrate binding site; other site 399804012161 Mg++ binding site; other site 399804012162 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 399804012163 active site 399804012164 substrate binding site [chemical binding]; other site 399804012165 CoA binding site [chemical binding]; other site 399804012166 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 399804012167 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 399804012168 gamma subunit interface [polypeptide binding]; other site 399804012169 epsilon subunit interface [polypeptide binding]; other site 399804012170 LBP interface [polypeptide binding]; other site 399804012171 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 399804012172 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 399804012173 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 399804012174 alpha subunit interaction interface [polypeptide binding]; other site 399804012175 Walker A motif; other site 399804012176 ATP binding site [chemical binding]; other site 399804012177 Walker B motif; other site 399804012178 inhibitor binding site; inhibition site 399804012179 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 399804012180 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 399804012181 core domain interface [polypeptide binding]; other site 399804012182 delta subunit interface [polypeptide binding]; other site 399804012183 epsilon subunit interface [polypeptide binding]; other site 399804012184 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 399804012185 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 399804012186 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 399804012187 beta subunit interaction interface [polypeptide binding]; other site 399804012188 Walker A motif; other site 399804012189 ATP binding site [chemical binding]; other site 399804012190 Walker B motif; other site 399804012191 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 399804012192 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 399804012193 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 399804012194 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 399804012195 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 399804012196 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 399804012197 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 399804012198 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 399804012199 ATP synthase I chain; Region: ATP_synt_I; cl09170 399804012200 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 399804012201 ParB-like nuclease domain; Region: ParBc; pfam02195 399804012202 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 399804012203 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 399804012204 P-loop; other site 399804012205 Magnesium ion binding site [ion binding]; other site 399804012206 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 399804012207 Magnesium ion binding site [ion binding]; other site 399804012208 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 399804012209 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 399804012210 S-adenosylmethionine binding site [chemical binding]; other site 399804012211 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 399804012212 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 399804012213 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 399804012214 FMN-binding protein MioC; Provisional; Region: PRK09004 399804012215 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 399804012216 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 399804012217 Protein export membrane protein; Region: SecD_SecF; cl14618 399804012218 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 399804012219 HlyD family secretion protein; Region: HlyD_3; pfam13437 399804012220 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 399804012221 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 399804012222 active site 399804012223 phosphorylation site [posttranslational modification] 399804012224 intermolecular recognition site; other site 399804012225 dimerization interface [polypeptide binding]; other site 399804012226 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 399804012227 DNA binding site [nucleotide binding] 399804012228 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 399804012229 HAMP domain; Region: HAMP; pfam00672 399804012230 dimerization interface [polypeptide binding]; other site 399804012231 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 399804012232 dimer interface [polypeptide binding]; other site 399804012233 phosphorylation site [posttranslational modification] 399804012234 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 399804012235 ATP binding site [chemical binding]; other site 399804012236 Mg2+ binding site [ion binding]; other site 399804012237 G-X-G motif; other site 399804012238 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 399804012239 Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient...; Region: SR_Res_par; cd03767 399804012240 catalytic residues [active] 399804012241 catalytic nucleophile [active] 399804012242 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 399804012243 HsdM N-terminal domain; Region: HsdM_N; pfam12161 399804012244 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 399804012245 Methyltransferase domain; Region: Methyltransf_26; pfam13659 399804012246 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 399804012247 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 399804012248 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 399804012249 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 399804012250 ATP binding site [chemical binding]; other site 399804012251 putative Mg++ binding site [ion binding]; other site 399804012252 Virulence protein [General function prediction only]; Region: COG3943 399804012253 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 399804012254 Helix-turn-helix domain; Region: HTH_17; pfam12728 399804012255 Domain of unknown function (DUF927); Region: DUF927; pfam06048 399804012256 Helix-turn-helix domain; Region: HTH_17; pfam12728 399804012257 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 399804012258 Transposase; Region: DEDD_Tnp_IS110; pfam01548 399804012259 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 399804012260 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 399804012261 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 399804012262 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 399804012263 Int/Topo IB signature motif; other site 399804012264 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 399804012265 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 399804012266 trmE is a tRNA modification GTPase; Region: trmE; cd04164 399804012267 G1 box; other site 399804012268 GTP/Mg2+ binding site [chemical binding]; other site 399804012269 Switch I region; other site 399804012270 G2 box; other site 399804012271 Switch II region; other site 399804012272 G3 box; other site 399804012273 G4 box; other site 399804012274 G5 box; other site 399804012275 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 399804012276 membrane protein insertase; Provisional; Region: PRK01318 399804012277 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 399804012278 Haemolytic domain; Region: Haemolytic; pfam01809 399804012279 ribonuclease P; Reviewed; Region: rnpA; PRK01732 399804012280 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399