-- dump date 20140619_055508 -- class Genbank::misc_feature -- table misc_feature_note -- id note 159087000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 159087000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 159087000003 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 159087000004 Walker A motif; other site 159087000005 ATP binding site [chemical binding]; other site 159087000006 Walker B motif; other site 159087000007 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 159087000008 arginine finger; other site 159087000009 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 159087000010 DnaA box-binding interface [nucleotide binding]; other site 159087000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 159087000012 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 159087000013 putative DNA binding surface [nucleotide binding]; other site 159087000014 dimer interface [polypeptide binding]; other site 159087000015 beta-clamp/clamp loader binding surface; other site 159087000016 beta-clamp/translesion DNA polymerase binding surface; other site 159087000017 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 159087000018 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 159087000019 ATP binding site [chemical binding]; other site 159087000020 Mg2+ binding site [ion binding]; other site 159087000021 G-X-G motif; other site 159087000022 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 159087000023 anchoring element; other site 159087000024 dimer interface [polypeptide binding]; other site 159087000025 ATP binding site [chemical binding]; other site 159087000026 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 159087000027 active site 159087000028 putative metal-binding site [ion binding]; other site 159087000029 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 159087000030 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 159087000031 HIT family signature motif; other site 159087000032 catalytic residue [active] 159087000033 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 159087000034 dimerization interface [polypeptide binding]; other site 159087000035 putative tRNAtyr binding site [nucleotide binding]; other site 159087000036 putative active site [active] 159087000037 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 159087000038 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087000039 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 159087000040 active site 159087000041 phosphorylation site [posttranslational modification] 159087000042 intermolecular recognition site; other site 159087000043 dimerization interface [polypeptide binding]; other site 159087000044 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087000045 Zn2+ binding site [ion binding]; other site 159087000046 Mg2+ binding site [ion binding]; other site 159087000047 Cache domain; Region: Cache_1; pfam02743 159087000048 PAS domain S-box; Region: sensory_box; TIGR00229 159087000049 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 159087000050 putative active site [active] 159087000051 heme pocket [chemical binding]; other site 159087000052 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087000053 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 159087000054 putative active site [active] 159087000055 heme pocket [chemical binding]; other site 159087000056 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 159087000057 dimer interface [polypeptide binding]; other site 159087000058 phosphorylation site [posttranslational modification] 159087000059 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 159087000060 ATP binding site [chemical binding]; other site 159087000061 Mg2+ binding site [ion binding]; other site 159087000062 G-X-G motif; other site 159087000063 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087000064 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 159087000065 active site 159087000066 phosphorylation site [posttranslational modification] 159087000067 intermolecular recognition site; other site 159087000068 dimerization interface [polypeptide binding]; other site 159087000069 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000070 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 159087000071 active site 159087000072 phosphorylation site [posttranslational modification] 159087000073 intermolecular recognition site; other site 159087000074 dimerization interface [polypeptide binding]; other site 159087000075 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 159087000076 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 159087000077 ApbE family; Region: ApbE; pfam02424 159087000078 glutathione synthetase; Provisional; Region: PRK05246 159087000079 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 159087000080 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 159087000081 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 159087000082 Glutamate-cysteine ligase; Region: GshA; pfam08886 159087000083 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000084 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 159087000085 active site 159087000086 phosphorylation site [posttranslational modification] 159087000087 intermolecular recognition site; other site 159087000088 dimerization interface [polypeptide binding]; other site 159087000089 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 159087000090 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087000091 Walker A/P-loop; other site 159087000092 ATP binding site [chemical binding]; other site 159087000093 Q-loop/lid; other site 159087000094 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087000095 ABC transporter; Region: ABC_tran_2; pfam12848 159087000096 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087000097 DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily; Region: SRPBCC_DUF1857; cd08863 159087000098 putative hydrophobic ligand binding site [chemical binding]; other site 159087000099 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 159087000100 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 159087000101 RNA binding surface [nucleotide binding]; other site 159087000102 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 159087000103 active site 159087000104 uracil binding [chemical binding]; other site 159087000105 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087000106 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087000107 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 159087000108 dimerization interface [polypeptide binding]; other site 159087000109 DNA topoisomerase III; Validated; Region: PRK08173 159087000110 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 159087000111 active site 159087000112 putative interdomain interaction site [polypeptide binding]; other site 159087000113 putative metal-binding site [ion binding]; other site 159087000114 putative nucleotide binding site [chemical binding]; other site 159087000115 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 159087000116 domain I; other site 159087000117 DNA binding groove [nucleotide binding] 159087000118 phosphate binding site [ion binding]; other site 159087000119 domain II; other site 159087000120 domain III; other site 159087000121 nucleotide binding site [chemical binding]; other site 159087000122 catalytic site [active] 159087000123 domain IV; other site 159087000124 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 159087000125 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 159087000126 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 159087000127 DNA protecting protein DprA; Region: dprA; TIGR00732 159087000128 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 159087000129 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 159087000130 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 159087000131 active site 159087000132 catalytic residues [active] 159087000133 metal binding site [ion binding]; metal-binding site 159087000134 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 159087000135 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 159087000136 putative active site [active] 159087000137 substrate binding site [chemical binding]; other site 159087000138 putative cosubstrate binding site; other site 159087000139 catalytic site [active] 159087000140 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 159087000141 substrate binding site [chemical binding]; other site 159087000142 M48 family peptidase; Provisional; Region: PRK03001 159087000143 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 159087000144 intracellular protease, PfpI family; Region: PfpI; TIGR01382 159087000145 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 159087000146 conserved cys residue [active] 159087000147 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; pfam02675 159087000148 S1/P1 nucleases and related enzymes; Region: S1-P1_nuclease; cd11010 159087000149 active site 159087000150 Zn binding site [ion binding]; other site 159087000151 16S rRNA methyltransferase B; Provisional; Region: PRK10901 159087000152 NusB family; Region: NusB; pfam01029 159087000153 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 159087000154 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 159087000155 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 159087000156 dimerization interface [polypeptide binding]; other site 159087000157 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 159087000158 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 159087000159 dimer interface [polypeptide binding]; other site 159087000160 phosphorylation site [posttranslational modification] 159087000161 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 159087000162 ATP binding site [chemical binding]; other site 159087000163 Mg2+ binding site [ion binding]; other site 159087000164 G-X-G motif; other site 159087000165 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087000166 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 159087000167 active site 159087000168 phosphorylation site [posttranslational modification] 159087000169 intermolecular recognition site; other site 159087000170 dimerization interface [polypeptide binding]; other site 159087000171 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087000172 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 159087000173 substrate binding site [chemical binding]; other site 159087000174 active site 159087000175 primosome assembly protein PriA; Validated; Region: PRK05580 159087000176 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 159087000177 ATP binding site [chemical binding]; other site 159087000178 putative Mg++ binding site [ion binding]; other site 159087000179 helicase superfamily c-terminal domain; Region: HELICc; smart00490 159087000180 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 159087000181 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087000182 putative substrate translocation pore; other site 159087000183 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 159087000184 MOSC domain; Region: MOSC; pfam03473 159087000185 fructokinase; Reviewed; Region: PRK09557 159087000186 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 159087000187 nucleotide binding site [chemical binding]; other site 159087000188 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 159087000189 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087000190 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 159087000191 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087000192 putative active site [active] 159087000193 heme pocket [chemical binding]; other site 159087000194 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087000195 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 159087000196 putative active site [active] 159087000197 heme pocket [chemical binding]; other site 159087000198 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 159087000199 dimer interface [polypeptide binding]; other site 159087000200 phosphorylation site [posttranslational modification] 159087000201 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 159087000202 ATP binding site [chemical binding]; other site 159087000203 Mg2+ binding site [ion binding]; other site 159087000204 G-X-G motif; other site 159087000205 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 159087000206 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000207 active site 159087000208 phosphorylation site [posttranslational modification] 159087000209 intermolecular recognition site; other site 159087000210 dimerization interface [polypeptide binding]; other site 159087000211 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000212 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 159087000213 active site 159087000214 phosphorylation site [posttranslational modification] 159087000215 intermolecular recognition site; other site 159087000216 dimerization interface [polypeptide binding]; other site 159087000217 Protein of unknown function (DUF861); Region: Cupin_3; cl17594 159087000218 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 159087000219 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 159087000220 active site 159087000221 metal binding site [ion binding]; metal-binding site 159087000222 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 159087000223 FAD binding domain; Region: FAD_binding_4; pfam01565 159087000224 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 159087000225 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 159087000226 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 159087000227 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 159087000228 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 159087000229 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 159087000230 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 159087000231 substrate binding pocket [chemical binding]; other site 159087000232 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 159087000233 B12 binding site [chemical binding]; other site 159087000234 cobalt ligand [ion binding]; other site 159087000235 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 159087000236 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 159087000237 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 159087000238 active site residue [active] 159087000239 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 159087000240 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 159087000241 putative substrate translocation pore; other site 159087000242 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 159087000243 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 159087000244 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 159087000245 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 159087000246 Membrane fusogenic activity; Region: BMFP; pfam04380 159087000247 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; pfam09694 159087000248 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 159087000249 Nitrogen regulatory protein P-II; Region: P-II; smart00938 159087000250 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 159087000251 Isochorismatase family; Region: Isochorismatase; pfam00857 159087000252 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 159087000253 catalytic triad [active] 159087000254 dimer interface [polypeptide binding]; other site 159087000255 conserved cis-peptide bond; other site 159087000256 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 159087000257 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 159087000258 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 159087000259 putative active site [active] 159087000260 putative substrate binding site [chemical binding]; other site 159087000261 putative cosubstrate binding site; other site 159087000262 catalytic site [active] 159087000263 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 159087000264 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 159087000265 motif II; other site 159087000266 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 159087000267 dimerization interface [polypeptide binding]; other site 159087000268 PAS domain; Region: PAS_9; pfam13426 159087000269 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087000270 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087000271 metal binding site [ion binding]; metal-binding site 159087000272 active site 159087000273 I-site; other site 159087000274 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 159087000275 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087000276 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 159087000277 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 159087000278 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087000279 Walker A/P-loop; other site 159087000280 ATP binding site [chemical binding]; other site 159087000281 Q-loop/lid; other site 159087000282 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087000283 ABC transporter; Region: ABC_tran_2; pfam12848 159087000284 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087000285 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 159087000286 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 159087000287 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087000288 Zn2+ binding site [ion binding]; other site 159087000289 Mg2+ binding site [ion binding]; other site 159087000290 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 159087000291 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 159087000292 minor groove reading motif; other site 159087000293 helix-hairpin-helix signature motif; other site 159087000294 substrate binding pocket [chemical binding]; other site 159087000295 active site 159087000296 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 159087000297 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 159087000298 DNA binding and oxoG recognition site [nucleotide binding] 159087000299 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 159087000300 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 159087000301 aromatic acid decarboxylase; Validated; Region: PRK05920 159087000302 Flavoprotein; Region: Flavoprotein; pfam02441 159087000303 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 159087000304 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 159087000305 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 159087000306 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 159087000307 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 159087000308 metal binding site [ion binding]; metal-binding site 159087000309 putative dimer interface [polypeptide binding]; other site 159087000310 urea carboxylase-associated protein 2; Region: urea_degr_2; TIGR03425 159087000311 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 159087000312 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 159087000313 Domain of unknown function (DUF1989); Region: DUF1989; pfam09347 159087000314 urea carboxylase; Region: urea_carbox; TIGR02712 159087000315 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087000316 ATP-grasp domain; Region: ATP-grasp_4; cl17255 159087000317 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 159087000318 Allophanate hydrolase subunit 2; Region: AHS2; smart00797 159087000319 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 159087000320 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 159087000321 carboxyltransferase (CT) interaction site; other site 159087000322 biotinylation site [posttranslational modification]; other site 159087000323 allophanate hydrolase; Provisional; Region: PRK08186 159087000324 Amidase; Region: Amidase; cl11426 159087000325 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 159087000326 Uncharacterized protein family (UPF0156); Region: RHH_2; cl17383 159087000327 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 159087000328 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 159087000329 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 159087000330 Creatinine amidohydrolase; Region: Creatininase; pfam02633 159087000331 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 159087000332 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 159087000333 Walker A/P-loop; other site 159087000334 ATP binding site [chemical binding]; other site 159087000335 Q-loop/lid; other site 159087000336 ABC transporter signature motif; other site 159087000337 Walker B; other site 159087000338 D-loop; other site 159087000339 H-loop/switch region; other site 159087000340 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 159087000341 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 159087000342 dimer interface [polypeptide binding]; other site 159087000343 conserved gate region; other site 159087000344 putative PBP binding loops; other site 159087000345 ABC-ATPase subunit interface; other site 159087000346 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 159087000347 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 159087000348 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087000349 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 159087000350 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 159087000351 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 159087000352 active site 159087000353 catalytic residues [active] 159087000354 metal binding site [ion binding]; metal-binding site 159087000355 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 159087000356 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087000357 NAD(P) binding site [chemical binding]; other site 159087000358 active site 159087000359 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 159087000360 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087000361 ATP-grasp domain; Region: ATP-grasp_4; cl17255 159087000362 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 159087000363 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 159087000364 carboxyltransferase (CT) interaction site; other site 159087000365 biotinylation site [posttranslational modification]; other site 159087000366 enoyl-CoA hydratase; Provisional; Region: PRK05995 159087000367 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 159087000368 substrate binding site [chemical binding]; other site 159087000369 oxyanion hole (OAH) forming residues; other site 159087000370 trimer interface [polypeptide binding]; other site 159087000371 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 159087000372 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 159087000373 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 159087000374 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 159087000375 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 159087000376 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 159087000377 putative catalytic residue [active] 159087000378 Uncharacterized conserved protein [Function unknown]; Region: COG1432 159087000379 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 159087000380 putative metal binding site [ion binding]; other site 159087000381 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 159087000382 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 159087000383 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087000384 active site 159087000385 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 159087000386 EamA-like transporter family; Region: EamA; pfam00892 159087000387 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 159087000388 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 159087000389 dimer interface [polypeptide binding]; other site 159087000390 active site 159087000391 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 159087000392 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087000393 Coenzyme A binding pocket [chemical binding]; other site 159087000394 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 159087000395 active site clefts [active] 159087000396 zinc binding site [ion binding]; other site 159087000397 dimer interface [polypeptide binding]; other site 159087000398 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 159087000399 isovaleryl-CoA dehydrogenase; Region: PLN02519 159087000400 substrate binding site [chemical binding]; other site 159087000401 FAD binding site [chemical binding]; other site 159087000402 catalytic base [active] 159087000403 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 159087000404 CoenzymeA binding site [chemical binding]; other site 159087000405 subunit interaction site [polypeptide binding]; other site 159087000406 PHB binding site; other site 159087000407 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 159087000408 DNA binding residues [nucleotide binding] 159087000409 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 159087000410 putative dimer interface [polypeptide binding]; other site 159087000411 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087000412 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 159087000413 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 159087000414 Ubiquitin-like proteins; Region: UBQ; cl00155 159087000415 PAS domain; Region: PAS; smart00091 159087000416 PAS domain; Region: PAS_9; pfam13426 159087000417 putative active site [active] 159087000418 heme pocket [chemical binding]; other site 159087000419 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 159087000420 SCP-2 sterol transfer family; Region: SCP2; cl01225 159087000421 putative protease; Provisional; Region: PRK15447 159087000422 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 159087000423 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 159087000424 Peptidase family U32; Region: Peptidase_U32; pfam01136 159087000425 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087000426 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 159087000427 active site 159087000428 phosphorylation site [posttranslational modification] 159087000429 intermolecular recognition site; other site 159087000430 dimerization interface [polypeptide binding]; other site 159087000431 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 159087000432 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 159087000433 rare lipoprotein A; Region: rlpA; TIGR00413 159087000434 Sporulation related domain; Region: SPOR; pfam05036 159087000435 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 159087000436 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 159087000437 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 159087000438 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 159087000439 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 159087000440 rod shape-determining protein MreC; Provisional; Region: PRK13922 159087000441 Protein of unknown function (DUF837); Region: DUF837; pfam05769 159087000442 rod shape-determining protein MreC; Region: MreC; pfam04085 159087000443 rod shape-determining protein MreB; Provisional; Region: PRK13927 159087000444 MreB and similar proteins; Region: MreB_like; cd10225 159087000445 nucleotide binding site [chemical binding]; other site 159087000446 Mg binding site [ion binding]; other site 159087000447 putative protofilament interaction site [polypeptide binding]; other site 159087000448 RodZ interaction site [polypeptide binding]; other site 159087000449 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 159087000450 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 159087000451 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 159087000452 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 159087000453 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 159087000454 GatB domain; Region: GatB_Yqey; smart00845 159087000455 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 159087000456 active site 159087000457 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 159087000458 putative active site [active] 159087000459 putative catalytic site [active] 159087000460 putative DNA binding site [nucleotide binding]; other site 159087000461 putative phosphate binding site [ion binding]; other site 159087000462 metal binding site A [ion binding]; metal-binding site 159087000463 putative AP binding site [nucleotide binding]; other site 159087000464 putative metal binding site B [ion binding]; other site 159087000465 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 159087000466 Protein of unknown function (DUF1469); Region: DUF1469; pfam07332 159087000467 YqjK-like protein; Region: YqjK; pfam13997 159087000468 muropeptide transporter; Reviewed; Region: ampG; PRK11902 159087000469 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 159087000470 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 159087000471 putative substrate translocation pore; other site 159087000472 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 159087000473 S-adenosylmethionine binding site [chemical binding]; other site 159087000474 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 159087000475 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 159087000476 PilZ domain; Region: PilZ; pfam07238 159087000477 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 159087000478 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 159087000479 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 159087000480 dimerization interface [polypeptide binding]; other site 159087000481 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087000482 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087000483 metal binding site [ion binding]; metal-binding site 159087000484 active site 159087000485 I-site; other site 159087000486 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 159087000487 ABC transporter substrate binding protein; Region: ABC_sub_bind; cl17301 159087000488 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 159087000489 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 159087000490 Cu(I) binding site [ion binding]; other site 159087000491 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 159087000492 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 159087000493 cobalamin binding residues [chemical binding]; other site 159087000494 putative BtuC binding residues; other site 159087000495 dimer interface [polypeptide binding]; other site 159087000496 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 159087000497 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 159087000498 cobalamin binding residues [chemical binding]; other site 159087000499 putative BtuC binding residues; other site 159087000500 dimer interface [polypeptide binding]; other site 159087000501 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 159087000502 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 159087000503 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087000504 homodimer interface [polypeptide binding]; other site 159087000505 catalytic residue [active] 159087000506 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 159087000507 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)...; Region: BluB; cd02145 159087000508 putative FMN binding site [chemical binding]; other site 159087000509 cobyric acid synthase; Provisional; Region: PRK00784 159087000510 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 159087000511 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 159087000512 catalytic triad [active] 159087000513 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 159087000514 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000515 active site 159087000516 phosphorylation site [posttranslational modification] 159087000517 intermolecular recognition site; other site 159087000518 dimerization interface [polypeptide binding]; other site 159087000519 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 159087000520 binding surface 159087000521 Tetratricopeptide repeat; Region: TPR_16; pfam13432 159087000522 TPR motif; other site 159087000523 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087000524 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 159087000525 ATP binding site [chemical binding]; other site 159087000526 Mg2+ binding site [ion binding]; other site 159087000527 G-X-G motif; other site 159087000528 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 159087000529 homotrimer interface [polypeptide binding]; other site 159087000530 Walker A motif; other site 159087000531 GTP binding site [chemical binding]; other site 159087000532 Walker B motif; other site 159087000533 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 159087000534 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 159087000535 putative dimer interface [polypeptide binding]; other site 159087000536 active site pocket [active] 159087000537 putative cataytic base [active] 159087000538 cobalamin synthase; Reviewed; Region: cobS; PRK00235 159087000539 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 159087000540 catalytic core [active] 159087000541 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087000542 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 159087000543 putative active site [active] 159087000544 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 159087000545 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 159087000546 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 159087000547 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 159087000548 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 159087000549 Walker A/P-loop; other site 159087000550 ATP binding site [chemical binding]; other site 159087000551 Q-loop/lid; other site 159087000552 ABC transporter signature motif; other site 159087000553 Walker B; other site 159087000554 D-loop; other site 159087000555 H-loop/switch region; other site 159087000556 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087000557 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 159087000558 Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli and similar proteins; Region: CE4_Ecf1_like_5s; cd10969 159087000559 putative active site [active] 159087000560 putative metal binding site [ion binding]; other site 159087000561 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087000562 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 159087000563 putative active site [active] 159087000564 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087000565 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 159087000566 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087000567 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 159087000568 putative active site [active] 159087000569 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 159087000570 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087000571 O-Antigen ligase; Region: Wzy_C; pfam04932 159087000572 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087000573 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 159087000574 putative active site [active] 159087000575 DNA polymerase I; Provisional; Region: PRK05755 159087000576 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 159087000577 active site 159087000578 metal binding site 1 [ion binding]; metal-binding site 159087000579 putative 5' ssDNA interaction site; other site 159087000580 metal binding site 3; metal-binding site 159087000581 metal binding site 2 [ion binding]; metal-binding site 159087000582 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 159087000583 putative DNA binding site [nucleotide binding]; other site 159087000584 putative metal binding site [ion binding]; other site 159087000585 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 159087000586 active site 159087000587 substrate binding site [chemical binding]; other site 159087000588 catalytic site [active] 159087000589 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 159087000590 active site 159087000591 DNA binding site [nucleotide binding] 159087000592 catalytic site [active] 159087000593 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 159087000594 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 159087000595 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 159087000596 putative active site [active] 159087000597 putative substrate binding site [chemical binding]; other site 159087000598 ATP binding site [chemical binding]; other site 159087000599 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 159087000600 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 159087000601 active site 159087000602 (T/H)XGH motif; other site 159087000603 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 159087000604 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 159087000605 Maf-like protein; Region: Maf; pfam02545 159087000606 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 159087000607 active site 159087000608 dimer interface [polypeptide binding]; other site 159087000609 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 159087000610 The adenylation (A) domain of siderophore-synthesizing nonribosomal peptide synthetases (NRPS); Region: A_NRPS_SidN3_like; cd05918 159087000611 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 159087000612 acyl-activating enzyme (AAE) consensus motif; other site 159087000613 AMP binding site [chemical binding]; other site 159087000614 non-ribosomal peptide synthetase terminal domain of unknown function; Region: NRPS_term_dom; TIGR02353 159087000615 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 159087000616 putative trimer interface [polypeptide binding]; other site 159087000617 putative CoA binding site [chemical binding]; other site 159087000618 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 159087000619 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 159087000620 putative trimer interface [polypeptide binding]; other site 159087000621 putative CoA binding site [chemical binding]; other site 159087000622 enoyl-CoA hydratase; Provisional; Region: PRK05862 159087000623 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 159087000624 substrate binding site [chemical binding]; other site 159087000625 oxyanion hole (OAH) forming residues; other site 159087000626 trimer interface [polypeptide binding]; other site 159087000627 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 159087000628 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 159087000629 acyl-activating enzyme (AAE) consensus motif; other site 159087000630 putative AMP binding site [chemical binding]; other site 159087000631 putative active site [active] 159087000632 putative CoA binding site [chemical binding]; other site 159087000633 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 159087000634 putative protease; Provisional; Region: PRK15452 159087000635 Peptidase family U32; Region: Peptidase_U32; pfam01136 159087000636 ribonuclease G; Provisional; Region: PRK11712 159087000637 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 159087000638 homodimer interface [polypeptide binding]; other site 159087000639 oligonucleotide binding site [chemical binding]; other site 159087000640 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 159087000641 Thiamine pyrophosphokinase; Region: TPK; cl08415 159087000642 dimerization interface [polypeptide binding]; other site 159087000643 ProQ/FINO family; Region: ProQ; smart00945 159087000644 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 159087000645 FAD binding site [chemical binding]; other site 159087000646 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; cl09940 159087000647 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 159087000648 RNA binding surface [nucleotide binding]; other site 159087000649 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 159087000650 Membrane protein of unknown function; Region: DUF360; pfam04020 159087000651 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 159087000652 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 159087000653 homotetramer interface [polypeptide binding]; other site 159087000654 ligand binding site [chemical binding]; other site 159087000655 catalytic site [active] 159087000656 NAD binding site [chemical binding]; other site 159087000657 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 159087000658 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 159087000659 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087000660 Zn2+ binding site [ion binding]; other site 159087000661 Mg2+ binding site [ion binding]; other site 159087000662 S-adenosylmethionine synthetase; Validated; Region: PRK05250 159087000663 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 159087000664 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 159087000665 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 159087000666 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 159087000667 putative acyl-acceptor binding pocket; other site 159087000668 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 159087000669 putative acyl-acceptor binding pocket; other site 159087000670 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 159087000671 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087000672 Coenzyme A binding pocket [chemical binding]; other site 159087000673 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 159087000674 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 159087000675 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 159087000676 Protein of unknown function, DUF484; Region: DUF484; cl17449 159087000677 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 159087000678 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 159087000679 active site 159087000680 DNA binding site [nucleotide binding] 159087000681 Int/Topo IB signature motif; other site 159087000682 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 159087000683 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 159087000684 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 159087000685 putative RNA binding site [nucleotide binding]; other site 159087000686 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 159087000687 S-adenosylmethionine binding site [chemical binding]; other site 159087000688 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 159087000689 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 159087000690 putative ligand binding site [chemical binding]; other site 159087000691 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087000692 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087000693 Walker A/P-loop; other site 159087000694 ATP binding site [chemical binding]; other site 159087000695 ABC transporter signature motif; other site 159087000696 Walker B; other site 159087000697 D-loop; other site 159087000698 H-loop/switch region; other site 159087000699 Translocation protein Sec62; Region: Sec62; cl02170 159087000700 Anti-anti-sigma regulatory factor (antagonist of anti-sigma factor) [Signal transduction mechanisms]; Region: SpoIIAA; COG1366 159087000701 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 159087000702 active site 159087000703 HslU subunit interaction site [polypeptide binding]; other site 159087000704 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 159087000705 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 159087000706 Walker A motif; other site 159087000707 ATP binding site [chemical binding]; other site 159087000708 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 159087000709 Walker B motif; other site 159087000710 arginine finger; other site 159087000711 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 159087000712 Predicted permeases [General function prediction only]; Region: COG0679 159087000713 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 159087000714 RNA binding surface [nucleotide binding]; other site 159087000715 diaminopimelate decarboxylase; Region: lysA; TIGR01048 159087000716 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 159087000717 active site 159087000718 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087000719 substrate binding site [chemical binding]; other site 159087000720 catalytic residues [active] 159087000721 dimer interface [polypeptide binding]; other site 159087000722 iron donor protein CyaY; Region: FeS_CyaY; TIGR03421 159087000723 putative iron binding site [ion binding]; other site 159087000724 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 159087000725 Transglycosylase; Region: Transgly; pfam00912 159087000726 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 159087000727 Cell division protein FtsA; Region: FtsA; cl17206 159087000728 Competence protein A; Region: Competence_A; pfam11104 159087000729 Cell division protein FtsA; Region: FtsA; pfam14450 159087000730 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 159087000731 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 159087000732 Pilus assembly protein, PilO; Region: PilO; pfam04350 159087000733 Pilus assembly protein, PilP; Region: PilP; pfam04351 159087000734 AMIN domain; Region: AMIN; pfam11741 159087000735 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 159087000736 Secretin and TonB N terminus short domain; Region: STN; smart00965 159087000737 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 159087000738 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087000739 shikimate kinase; Reviewed; Region: aroK; PRK00131 159087000740 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 159087000741 ADP binding site [chemical binding]; other site 159087000742 magnesium binding site [ion binding]; other site 159087000743 putative shikimate binding site; other site 159087000744 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 159087000745 active site 159087000746 dimer interface [polypeptide binding]; other site 159087000747 metal binding site [ion binding]; metal-binding site 159087000748 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 159087000749 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 159087000750 active site 159087000751 dimer interface [polypeptide binding]; other site 159087000752 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 159087000753 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 159087000754 active site 159087000755 FMN binding site [chemical binding]; other site 159087000756 substrate binding site [chemical binding]; other site 159087000757 3Fe-4S cluster binding site [ion binding]; other site 159087000758 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 159087000759 domain interface; other site 159087000760 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 159087000761 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 159087000762 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 159087000763 Substrate binding site; other site 159087000764 Mg++ binding site; other site 159087000765 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 159087000766 active site 159087000767 substrate binding site [chemical binding]; other site 159087000768 CoA binding site [chemical binding]; other site 159087000769 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 159087000770 elongation factor G; Reviewed; Region: PRK12740 159087000771 G1 box; other site 159087000772 putative GEF interaction site [polypeptide binding]; other site 159087000773 GTP/Mg2+ binding site [chemical binding]; other site 159087000774 Switch I region; other site 159087000775 G2 box; other site 159087000776 G3 box; other site 159087000777 Switch II region; other site 159087000778 G4 box; other site 159087000779 G5 box; other site 159087000780 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 159087000781 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 159087000782 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 159087000783 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 159087000784 PAS domain; Region: PAS_9; pfam13426 159087000785 putative active site [active] 159087000786 heme pocket [chemical binding]; other site 159087000787 Cache domain; Region: Cache_1; pfam02743 159087000788 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087000789 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 159087000790 dimer interface [polypeptide binding]; other site 159087000791 phosphorylation site [posttranslational modification] 159087000792 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 159087000793 ATP binding site [chemical binding]; other site 159087000794 Mg2+ binding site [ion binding]; other site 159087000795 G-X-G motif; other site 159087000796 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000797 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 159087000798 active site 159087000799 phosphorylation site [posttranslational modification] 159087000800 intermolecular recognition site; other site 159087000801 dimerization interface [polypeptide binding]; other site 159087000802 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087000803 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 159087000804 active site 159087000805 phosphorylation site [posttranslational modification] 159087000806 intermolecular recognition site; other site 159087000807 dimerization interface [polypeptide binding]; other site 159087000808 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087000809 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 159087000810 active site 159087000811 phosphorylation site [posttranslational modification] 159087000812 intermolecular recognition site; other site 159087000813 dimerization interface [polypeptide binding]; other site 159087000814 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 159087000815 DNA binding site [nucleotide binding] 159087000816 PAS fold; Region: PAS_7; pfam12860 159087000817 PAS fold; Region: PAS_4; pfam08448 159087000818 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 159087000819 putative active site [active] 159087000820 heme pocket [chemical binding]; other site 159087000821 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087000822 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 159087000823 dimer interface [polypeptide binding]; other site 159087000824 phosphorylation site [posttranslational modification] 159087000825 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 159087000826 ATP binding site [chemical binding]; other site 159087000827 Mg2+ binding site [ion binding]; other site 159087000828 G-X-G motif; other site 159087000829 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000830 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 159087000831 active site 159087000832 phosphorylation site [posttranslational modification] 159087000833 intermolecular recognition site; other site 159087000834 dimerization interface [polypeptide binding]; other site 159087000835 acyl-CoA synthetase; Validated; Region: PRK08162 159087000836 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 159087000837 acyl-activating enzyme (AAE) consensus motif; other site 159087000838 putative active site [active] 159087000839 AMP binding site [chemical binding]; other site 159087000840 putative CoA binding site [chemical binding]; other site 159087000841 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 159087000842 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 159087000843 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087000844 active site 159087000845 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 159087000846 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 159087000847 hydroxyglutarate oxidase; Provisional; Region: PRK11728 159087000848 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 159087000849 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 159087000850 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 159087000851 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087000852 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087000853 metal binding site [ion binding]; metal-binding site 159087000854 active site 159087000855 I-site; other site 159087000856 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 159087000857 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 159087000858 Walker A motif; other site 159087000859 ATP binding site [chemical binding]; other site 159087000860 Walker B motif; other site 159087000861 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 159087000862 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 159087000863 dimer interface [polypeptide binding]; other site 159087000864 phosphorylation site [posttranslational modification] 159087000865 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 159087000866 ATP binding site [chemical binding]; other site 159087000867 Mg2+ binding site [ion binding]; other site 159087000868 G-X-G motif; other site 159087000869 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000870 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 159087000871 active site 159087000872 phosphorylation site [posttranslational modification] 159087000873 intermolecular recognition site; other site 159087000874 dimerization interface [polypeptide binding]; other site 159087000875 phosphoglyceromutase; Provisional; Region: PRK05434 159087000876 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 159087000877 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 159087000878 phosphatidylinositol kinase; Provisional; Region: PTZ00303 159087000879 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 159087000880 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 159087000881 putative active site [active] 159087000882 catalytic site [active] 159087000883 putative metal binding site [ion binding]; other site 159087000884 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 159087000885 Protein of unknown function (DUF1439); Region: DUF1439; pfam07273 159087000886 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087000887 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 159087000888 dimerization interface [polypeptide binding]; other site 159087000889 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 159087000890 dimer interface [polypeptide binding]; other site 159087000891 phosphorylation site [posttranslational modification] 159087000892 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 159087000893 ATP binding site [chemical binding]; other site 159087000894 Mg2+ binding site [ion binding]; other site 159087000895 G-X-G motif; other site 159087000896 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000897 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 159087000898 active site 159087000899 phosphorylation site [posttranslational modification] 159087000900 intermolecular recognition site; other site 159087000901 dimerization interface [polypeptide binding]; other site 159087000902 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000903 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 159087000904 active site 159087000905 phosphorylation site [posttranslational modification] 159087000906 intermolecular recognition site; other site 159087000907 dimerization interface [polypeptide binding]; other site 159087000908 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 159087000909 putative binding surface; other site 159087000910 active site 159087000911 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087000912 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 159087000913 substrate binding pocket [chemical binding]; other site 159087000914 membrane-bound complex binding site; other site 159087000915 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 159087000916 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 159087000917 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087000918 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 159087000919 B12 binding site [chemical binding]; other site 159087000920 cobalt ligand [ion binding]; other site 159087000921 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 159087000922 Walker A; other site 159087000923 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, unknown subfamily 1; composed of uncharacterized bacterial proteins containing a C-terminal MCM domain. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The...; Region: MM_CoA_mutase_1; cd03678 159087000924 putative active site [active] 159087000925 putative substrate binding site [chemical binding]; other site 159087000926 putative coenzyme B12 binding site [chemical binding]; other site 159087000927 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 159087000928 Cache domain; Region: Cache_2; cl07034 159087000929 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 159087000930 PAS domain; Region: PAS_9; pfam13426 159087000931 putative active site [active] 159087000932 heme pocket [chemical binding]; other site 159087000933 PAS fold; Region: PAS_4; pfam08448 159087000934 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 159087000935 dimer interface [polypeptide binding]; other site 159087000936 phosphorylation site [posttranslational modification] 159087000937 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 159087000938 ATP binding site [chemical binding]; other site 159087000939 Mg2+ binding site [ion binding]; other site 159087000940 G-X-G motif; other site 159087000941 Response regulator receiver domain; Region: Response_reg; pfam00072 159087000942 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 159087000943 active site 159087000944 phosphorylation site [posttranslational modification] 159087000945 intermolecular recognition site; other site 159087000946 dimerization interface [polypeptide binding]; other site 159087000947 Autotransporter beta-domain; Region: Autotransporter; smart00869 159087000948 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 159087000949 Peptidase family M48; Region: Peptidase_M48; cl12018 159087000950 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 159087000951 binding surface 159087000952 TPR motif; other site 159087000953 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087000954 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 159087000955 ligand binding site [chemical binding]; other site 159087000956 flexible hinge region; other site 159087000957 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 159087000958 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 159087000959 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087000960 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 159087000961 acyl-activating enzyme (AAE) consensus motif; other site 159087000962 putative AMP binding site [chemical binding]; other site 159087000963 putative active site [active] 159087000964 putative CoA binding site [chemical binding]; other site 159087000965 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087000966 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087000967 Walker A/P-loop; other site 159087000968 ATP binding site [chemical binding]; other site 159087000969 Q-loop/lid; other site 159087000970 ABC transporter signature motif; other site 159087000971 Walker B; other site 159087000972 D-loop; other site 159087000973 H-loop/switch region; other site 159087000974 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 159087000975 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087000976 TM-ABC transporter signature motif; other site 159087000977 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087000978 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087000979 TM-ABC transporter signature motif; other site 159087000980 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 159087000981 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 159087000982 putative ligand binding site [chemical binding]; other site 159087000983 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087000984 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087000985 Walker A/P-loop; other site 159087000986 ATP binding site [chemical binding]; other site 159087000987 Q-loop/lid; other site 159087000988 ABC transporter signature motif; other site 159087000989 Walker B; other site 159087000990 D-loop; other site 159087000991 H-loop/switch region; other site 159087000992 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 159087000993 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087000994 acyl-activating enzyme (AAE) consensus motif; other site 159087000995 active site 159087000996 AMP binding site [chemical binding]; other site 159087000997 CoA binding site [chemical binding]; other site 159087000998 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 159087000999 CoA-transferase family III; Region: CoA_transf_3; pfam02515 159087001000 cyclase homology domain; Region: CHD; cd07302 159087001001 metal binding site [ion binding]; metal-binding site 159087001002 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 159087001003 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 159087001004 phosphopeptide binding site; other site 159087001005 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 159087001006 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 159087001007 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 159087001008 Predicted permeases [General function prediction only]; Region: COG0679 159087001009 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087001010 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 159087001011 active site 159087001012 phosphorylation site [posttranslational modification] 159087001013 intermolecular recognition site; other site 159087001014 dimerization interface [polypeptide binding]; other site 159087001015 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 159087001016 DNA binding residues [nucleotide binding] 159087001017 dimerization interface [polypeptide binding]; other site 159087001018 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087001019 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 159087001020 dimer interface [polypeptide binding]; other site 159087001021 phosphorylation site [posttranslational modification] 159087001022 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 159087001023 ATP binding site [chemical binding]; other site 159087001024 Mg2+ binding site [ion binding]; other site 159087001025 G-X-G motif; other site 159087001026 Methyltransferase domain; Region: Methyltransf_18; pfam12847 159087001027 S-adenosylmethionine binding site [chemical binding]; other site 159087001028 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 159087001029 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 159087001030 dimer interface [polypeptide binding]; other site 159087001031 PYR/PP interface [polypeptide binding]; other site 159087001032 TPP binding site [chemical binding]; other site 159087001033 substrate binding site [chemical binding]; other site 159087001034 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 159087001035 TPP-binding site; other site 159087001036 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 159087001037 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087001038 FAD binding domain; Region: FAD_binding_4; pfam01565 159087001039 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 159087001040 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087001041 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 159087001042 dimerization interface [polypeptide binding]; other site 159087001043 ligand binding site [chemical binding]; other site 159087001044 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 159087001045 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087001046 TM-ABC transporter signature motif; other site 159087001047 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087001048 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087001049 TM-ABC transporter signature motif; other site 159087001050 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087001051 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087001052 Walker A/P-loop; other site 159087001053 ATP binding site [chemical binding]; other site 159087001054 Q-loop/lid; other site 159087001055 ABC transporter signature motif; other site 159087001056 Walker B; other site 159087001057 D-loop; other site 159087001058 H-loop/switch region; other site 159087001059 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087001060 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087001061 Walker A/P-loop; other site 159087001062 ATP binding site [chemical binding]; other site 159087001063 Q-loop/lid; other site 159087001064 ABC transporter signature motif; other site 159087001065 Walker B; other site 159087001066 D-loop; other site 159087001067 H-loop/switch region; other site 159087001068 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 159087001069 septum formation inhibitor; Reviewed; Region: minC; PRK03511 159087001070 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 159087001071 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 159087001072 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 159087001073 Switch I; other site 159087001074 Switch II; other site 159087001075 cell division topological specificity factor MinE; Provisional; Region: PRK13989 159087001076 Predicted membrane protein [Function unknown]; Region: COG3650 159087001077 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087001078 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 159087001079 catalytic loop [active] 159087001080 iron binding site [ion binding]; other site 159087001081 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 159087001082 FAD binding pocket [chemical binding]; other site 159087001083 FAD binding motif [chemical binding]; other site 159087001084 phosphate binding motif [ion binding]; other site 159087001085 beta-alpha-beta structure motif; other site 159087001086 NAD binding pocket [chemical binding]; other site 159087001087 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 159087001088 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 159087001089 putative NAD(P) binding site [chemical binding]; other site 159087001090 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 159087001091 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 159087001092 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 159087001093 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 159087001094 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 159087001095 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 159087001096 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 159087001097 Glycine-zipper containing OmpA-like membrane domain; Region: Gly-zipper_OmpA; pfam13436 159087001098 lipoyl synthase; Provisional; Region: PRK05481 159087001099 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 159087001100 FeS/SAM binding site; other site 159087001101 lipoate-protein ligase B; Provisional; Region: PRK14342 159087001102 Protein of unknown function (DUF493); Region: DUF493; pfam04359 159087001103 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 159087001104 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 159087001105 homodimer interface [polypeptide binding]; other site 159087001106 substrate-cofactor binding pocket; other site 159087001107 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087001108 catalytic residue [active] 159087001109 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 159087001110 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 159087001111 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 159087001112 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 159087001113 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087001114 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 159087001115 dimerization interface [polypeptide binding]; other site 159087001116 heat shock protein HtpX; Provisional; Region: PRK05457 159087001117 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 159087001118 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087001119 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087001120 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087001121 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087001122 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 159087001123 Nitrogen regulatory protein P-II; Region: P-II; smart00938 159087001124 GAF domain; Region: GAF; pfam01590 159087001125 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087001126 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 159087001127 PAS domain; Region: PAS_9; pfam13426 159087001128 putative active site [active] 159087001129 heme pocket [chemical binding]; other site 159087001130 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 159087001131 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 159087001132 dimer interface [polypeptide binding]; other site 159087001133 substrate binding site [chemical binding]; other site 159087001134 metal binding site [ion binding]; metal-binding site 159087001135 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 159087001136 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 159087001137 LysE type translocator; Region: LysE; cl00565 159087001138 Cytochrome c; Region: Cytochrom_C; cl11414 159087001139 elongation factor Tu; Reviewed; Region: PRK00049 159087001140 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 159087001141 G1 box; other site 159087001142 GEF interaction site [polypeptide binding]; other site 159087001143 GTP/Mg2+ binding site [chemical binding]; other site 159087001144 Switch I region; other site 159087001145 G2 box; other site 159087001146 G3 box; other site 159087001147 Switch II region; other site 159087001148 G4 box; other site 159087001149 G5 box; other site 159087001150 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 159087001151 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 159087001152 Antibiotic Binding Site [chemical binding]; other site 159087001153 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 159087001154 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 159087001155 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 159087001156 putative homodimer interface [polypeptide binding]; other site 159087001157 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 159087001158 heterodimer interface [polypeptide binding]; other site 159087001159 homodimer interface [polypeptide binding]; other site 159087001160 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 159087001161 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 159087001162 23S rRNA interface [nucleotide binding]; other site 159087001163 L7/L12 interface [polypeptide binding]; other site 159087001164 putative thiostrepton binding site; other site 159087001165 L25 interface [polypeptide binding]; other site 159087001166 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 159087001167 mRNA/rRNA interface [nucleotide binding]; other site 159087001168 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 159087001169 23S rRNA interface [nucleotide binding]; other site 159087001170 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 159087001171 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 159087001172 core dimer interface [polypeptide binding]; other site 159087001173 peripheral dimer interface [polypeptide binding]; other site 159087001174 L10 interface [polypeptide binding]; other site 159087001175 L11 interface [polypeptide binding]; other site 159087001176 putative EF-Tu interaction site [polypeptide binding]; other site 159087001177 putative EF-G interaction site [polypeptide binding]; other site 159087001178 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 159087001179 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 159087001180 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 159087001181 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 159087001182 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 159087001183 RPB3 interaction site [polypeptide binding]; other site 159087001184 RPB1 interaction site [polypeptide binding]; other site 159087001185 RPB11 interaction site [polypeptide binding]; other site 159087001186 RPB10 interaction site [polypeptide binding]; other site 159087001187 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 159087001188 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 159087001189 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 159087001190 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 159087001191 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 159087001192 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 159087001193 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 159087001194 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 159087001195 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 159087001196 DNA binding site [nucleotide binding] 159087001197 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 159087001198 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 159087001199 S17 interaction site [polypeptide binding]; other site 159087001200 S8 interaction site; other site 159087001201 16S rRNA interaction site [nucleotide binding]; other site 159087001202 streptomycin interaction site [chemical binding]; other site 159087001203 23S rRNA interaction site [nucleotide binding]; other site 159087001204 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 159087001205 30S ribosomal protein S7; Validated; Region: PRK05302 159087001206 elongation factor G; Reviewed; Region: PRK00007 159087001207 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 159087001208 G1 box; other site 159087001209 putative GEF interaction site [polypeptide binding]; other site 159087001210 GTP/Mg2+ binding site [chemical binding]; other site 159087001211 Switch I region; other site 159087001212 G2 box; other site 159087001213 G3 box; other site 159087001214 Switch II region; other site 159087001215 G4 box; other site 159087001216 G5 box; other site 159087001217 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 159087001218 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 159087001219 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 159087001220 elongation factor Tu; Reviewed; Region: PRK00049 159087001221 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 159087001222 G1 box; other site 159087001223 GEF interaction site [polypeptide binding]; other site 159087001224 GTP/Mg2+ binding site [chemical binding]; other site 159087001225 Switch I region; other site 159087001226 G2 box; other site 159087001227 G3 box; other site 159087001228 Switch II region; other site 159087001229 G4 box; other site 159087001230 G5 box; other site 159087001231 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 159087001232 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 159087001233 Antibiotic Binding Site [chemical binding]; other site 159087001234 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 159087001235 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 159087001236 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 159087001237 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 159087001238 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 159087001239 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 159087001240 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 159087001241 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 159087001242 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 159087001243 putative translocon binding site; other site 159087001244 protein-rRNA interface [nucleotide binding]; other site 159087001245 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 159087001246 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 159087001247 G-X-X-G motif; other site 159087001248 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 159087001249 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 159087001250 23S rRNA interface [nucleotide binding]; other site 159087001251 5S rRNA interface [nucleotide binding]; other site 159087001252 putative antibiotic binding site [chemical binding]; other site 159087001253 L25 interface [polypeptide binding]; other site 159087001254 L27 interface [polypeptide binding]; other site 159087001255 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 159087001256 23S rRNA interface [nucleotide binding]; other site 159087001257 putative translocon interaction site; other site 159087001258 signal recognition particle (SRP54) interaction site; other site 159087001259 L23 interface [polypeptide binding]; other site 159087001260 trigger factor interaction site; other site 159087001261 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 159087001262 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 159087001263 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 159087001264 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 159087001265 RNA binding site [nucleotide binding]; other site 159087001266 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 159087001267 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 159087001268 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 159087001269 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 159087001270 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 159087001271 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 159087001272 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 159087001273 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 159087001274 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 159087001275 5S rRNA interface [nucleotide binding]; other site 159087001276 23S rRNA interface [nucleotide binding]; other site 159087001277 L5 interface [polypeptide binding]; other site 159087001278 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 159087001279 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 159087001280 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 159087001281 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 159087001282 23S rRNA binding site [nucleotide binding]; other site 159087001283 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 159087001284 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 159087001285 SecY translocase; Region: SecY; pfam00344 159087001286 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 159087001287 rRNA binding site [nucleotide binding]; other site 159087001288 predicted 30S ribosome binding site; other site 159087001289 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 159087001290 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 159087001291 30S ribosomal protein S13; Region: bact_S13; TIGR03631 159087001292 30S ribosomal protein S11; Validated; Region: PRK05309 159087001293 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 159087001294 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 159087001295 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 159087001296 RNA binding surface [nucleotide binding]; other site 159087001297 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 159087001298 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 159087001299 alphaNTD homodimer interface [polypeptide binding]; other site 159087001300 alphaNTD - beta interaction site [polypeptide binding]; other site 159087001301 alphaNTD - beta' interaction site [polypeptide binding]; other site 159087001302 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 159087001303 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 159087001304 Response regulator receiver domain; Region: Response_reg; pfam00072 159087001305 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 159087001306 active site 159087001307 phosphorylation site [posttranslational modification] 159087001308 intermolecular recognition site; other site 159087001309 dimerization interface [polypeptide binding]; other site 159087001310 PAS domain S-box; Region: sensory_box; TIGR00229 159087001311 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 159087001312 putative active site [active] 159087001313 heme pocket [chemical binding]; other site 159087001314 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 159087001315 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 159087001316 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 159087001317 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087001318 Walker A/P-loop; other site 159087001319 ATP binding site [chemical binding]; other site 159087001320 Q-loop/lid; other site 159087001321 ABC transporter signature motif; other site 159087001322 Walker B; other site 159087001323 D-loop; other site 159087001324 H-loop/switch region; other site 159087001325 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 159087001326 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 159087001327 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 159087001328 Sporulation related domain; Region: SPOR; pfam05036 159087001329 TPR repeat; Region: TPR_11; pfam13414 159087001330 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 159087001331 binding surface 159087001332 TPR motif; other site 159087001333 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 159087001334 homotrimer interaction site [polypeptide binding]; other site 159087001335 putative active site [active] 159087001336 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 159087001337 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 159087001338 generic binding surface II; other site 159087001339 ssDNA binding site; other site 159087001340 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 159087001341 ATP binding site [chemical binding]; other site 159087001342 putative Mg++ binding site [ion binding]; other site 159087001343 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 159087001344 nucleotide binding region [chemical binding]; other site 159087001345 ATP-binding site [chemical binding]; other site 159087001346 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087001347 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087001348 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 159087001349 dimerization interface [polypeptide binding]; other site 159087001350 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 159087001351 putative substrate translocation pore; other site 159087001352 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087001353 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 159087001354 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 159087001355 NADP binding site [chemical binding]; other site 159087001356 dimer interface [polypeptide binding]; other site 159087001357 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 159087001358 active site 1 [active] 159087001359 dimer interface [polypeptide binding]; other site 159087001360 hexamer interface [polypeptide binding]; other site 159087001361 active site 2 [active] 159087001362 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 159087001363 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 159087001364 active site 159087001365 FMN binding site [chemical binding]; other site 159087001366 substrate binding site [chemical binding]; other site 159087001367 homotetramer interface [polypeptide binding]; other site 159087001368 catalytic residue [active] 159087001369 Flagellin N-methylase; Region: FliB; cl00497 159087001370 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 159087001371 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 159087001372 PGAP1-like protein; Region: PGAP1; pfam07819 159087001373 Hemerythrin-like domain; Region: Hr-like; cd12108 159087001374 Fe binding site [ion binding]; other site 159087001375 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087001376 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087001377 Walker A/P-loop; other site 159087001378 ATP binding site [chemical binding]; other site 159087001379 Q-loop/lid; other site 159087001380 ABC transporter signature motif; other site 159087001381 Walker B; other site 159087001382 D-loop; other site 159087001383 H-loop/switch region; other site 159087001384 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087001385 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087001386 Walker A/P-loop; other site 159087001387 ATP binding site [chemical binding]; other site 159087001388 Q-loop/lid; other site 159087001389 ABC transporter signature motif; other site 159087001390 Walker B; other site 159087001391 D-loop; other site 159087001392 H-loop/switch region; other site 159087001393 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087001394 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087001395 TM-ABC transporter signature motif; other site 159087001396 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 159087001397 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087001398 TM-ABC transporter signature motif; other site 159087001399 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087001400 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 159087001401 catalytic loop [active] 159087001402 iron binding site [ion binding]; other site 159087001403 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S]...; Region: O2ase_reductase_like; cd06187 159087001404 FAD binding pocket [chemical binding]; other site 159087001405 FAD binding motif [chemical binding]; other site 159087001406 phosphate binding motif [ion binding]; other site 159087001407 beta-alpha-beta structure motif; other site 159087001408 NAD binding pocket [chemical binding]; other site 159087001409 phenylacetic acid degradation protein paaN; Region: PaaN_2; TIGR02288 159087001410 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 159087001411 NAD(P) binding site [chemical binding]; other site 159087001412 catalytic residues [active] 159087001413 enoyl-CoA hydratase; Provisional; Region: PRK08140 159087001414 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 159087001415 substrate binding site [chemical binding]; other site 159087001416 oxyanion hole (OAH) forming residues; other site 159087001417 trimer interface [polypeptide binding]; other site 159087001418 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 159087001419 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 159087001420 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087001421 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087001422 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 159087001423 CoenzymeA binding site [chemical binding]; other site 159087001424 subunit interaction site [polypeptide binding]; other site 159087001425 PHB binding site; other site 159087001426 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087001427 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 159087001428 acyl-activating enzyme (AAE) consensus motif; other site 159087001429 AMP binding site [chemical binding]; other site 159087001430 active site 159087001431 CoA binding site [chemical binding]; other site 159087001432 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 159087001433 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 159087001434 dimer interface [polypeptide binding]; other site 159087001435 active site 159087001436 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087001437 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087001438 putative ligand binding site [chemical binding]; other site 159087001439 phenylacetate-CoA oxygenase subunit PaaA; Provisional; Region: paaA; PRK13778 159087001440 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 159087001441 phenylacetate-CoA oxygenase subunit PaaB; Provisional; Region: paaB; PRK13781 159087001442 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; pfam05138 159087001443 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 159087001444 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 159087001445 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 159087001446 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 159087001447 FAD binding pocket [chemical binding]; other site 159087001448 FAD binding motif [chemical binding]; other site 159087001449 phosphate binding motif [ion binding]; other site 159087001450 beta-alpha-beta structure motif; other site 159087001451 NAD(p) ribose binding residues [chemical binding]; other site 159087001452 NAD binding pocket [chemical binding]; other site 159087001453 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 159087001454 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 159087001455 catalytic loop [active] 159087001456 iron binding site [ion binding]; other site 159087001457 enoyl-CoA hydratase; Provisional; Region: PRK05862 159087001458 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 159087001459 substrate binding site [chemical binding]; other site 159087001460 oxyanion hole (OAH) forming residues; other site 159087001461 trimer interface [polypeptide binding]; other site 159087001462 enoyl-CoA hydratase; Provisional; Region: PRK05995 159087001463 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 159087001464 substrate binding site [chemical binding]; other site 159087001465 oxyanion hole (OAH) forming residues; other site 159087001466 trimer interface [polypeptide binding]; other site 159087001467 Transcriptional regulator [Transcription]; Region: IclR; COG1414 159087001468 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 159087001469 Bacterial transcriptional regulator; Region: IclR; pfam01614 159087001470 phenylacetic acid degradation protein PaaY; Region: PaaY; TIGR02287 159087001471 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 159087001472 putative trimer interface [polypeptide binding]; other site 159087001473 putative metal binding site [ion binding]; other site 159087001474 PaaX-like protein; Region: PaaX; pfam07848 159087001475 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 159087001476 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 159087001477 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 159087001478 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 159087001479 MG2 domain; Region: A2M_N; pfam01835 159087001480 Alpha-2-macroglobulin family; Region: A2M; pfam00207 159087001481 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 159087001482 surface patch; other site 159087001483 thioester region; other site 159087001484 specificity defining residues; other site 159087001485 penicillin-binding protein 1C; Provisional; Region: PRK11240 159087001486 Transglycosylase; Region: Transgly; pfam00912 159087001487 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 159087001488 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 159087001489 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 159087001490 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 159087001491 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087001492 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 159087001493 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; pfam10106 159087001494 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 159087001495 Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Region: PLDc_vPLD1_2_like_1; cd09104 159087001496 putative active site [active] 159087001497 catalytic site [active] 159087001498 Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins; Region: PLDc_vPLD1_2_yPLD_like_2; cd09141 159087001499 putative active site [active] 159087001500 catalytic site [active] 159087001501 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 159087001502 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 159087001503 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087001504 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 159087001505 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; pfam10106 159087001506 Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Region: PLDc_vPLD1_2_like_1; cd09104 159087001507 putative active site [active] 159087001508 catalytic site [active] 159087001509 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 159087001510 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 159087001511 Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins; Region: PLDc_vPLD1_2_yPLD_like_2; cd09141 159087001512 putative active site [active] 159087001513 catalytic site [active] 159087001514 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 159087001515 putative active site [active] 159087001516 catalytic site [active] 159087001517 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 159087001518 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 159087001519 dimerization interface [polypeptide binding]; other site 159087001520 putative DNA binding site [nucleotide binding]; other site 159087001521 putative Zn2+ binding site [ion binding]; other site 159087001522 bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase; Validated; Region: PRK08043 159087001523 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087001524 putative acyl-acceptor binding pocket; other site 159087001525 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 159087001526 acyl-activating enzyme (AAE) consensus motif; other site 159087001527 putative AMP binding site [chemical binding]; other site 159087001528 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 159087001529 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 159087001530 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087001531 putative acyl-acceptor binding pocket; other site 159087001532 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 159087001533 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG1964 159087001534 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 159087001535 FeS/SAM binding site; other site 159087001536 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 159087001537 PAS fold; Region: PAS_3; pfam08447 159087001538 putative active site [active] 159087001539 heme pocket [chemical binding]; other site 159087001540 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087001541 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087001542 metal binding site [ion binding]; metal-binding site 159087001543 active site 159087001544 I-site; other site 159087001545 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 159087001546 UbiA prenyltransferase family; Region: UbiA; pfam01040 159087001547 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 159087001548 modified peptide precursor CbpA; Region: cobo_pep; TIGR04164 159087001549 peptide-modifying radical SAM enzyme CbpB; Region: rSAM_cobopep; TIGR04163 159087001550 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 159087001551 FeS/SAM binding site; other site 159087001552 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 159087001553 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 159087001554 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087001555 Coenzyme A binding pocket [chemical binding]; other site 159087001556 Predicted membrane protein [Function unknown]; Region: COG3671 159087001557 PAS domain S-box; Region: sensory_box; TIGR00229 159087001558 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087001559 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 159087001560 dimer interface [polypeptide binding]; other site 159087001561 phosphorylation site [posttranslational modification] 159087001562 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 159087001563 ATP binding site [chemical binding]; other site 159087001564 Mg2+ binding site [ion binding]; other site 159087001565 G-X-G motif; other site 159087001566 Response regulator receiver domain; Region: Response_reg; pfam00072 159087001567 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 159087001568 active site 159087001569 phosphorylation site [posttranslational modification] 159087001570 intermolecular recognition site; other site 159087001571 dimerization interface [polypeptide binding]; other site 159087001572 Uncharacterized conserved protein [Function unknown]; Region: COG1284 159087001573 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 159087001574 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 159087001575 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 159087001576 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087001577 PAS domain S-box; Region: sensory_box; TIGR00229 159087001578 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 159087001579 putative active site [active] 159087001580 heme pocket [chemical binding]; other site 159087001581 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 159087001582 PAS domain; Region: PAS_9; pfam13426 159087001583 putative active site [active] 159087001584 heme pocket [chemical binding]; other site 159087001585 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087001586 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087001587 metal binding site [ion binding]; metal-binding site 159087001588 active site 159087001589 I-site; other site 159087001590 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 159087001591 oligomerisation interface [polypeptide binding]; other site 159087001592 mobile loop; other site 159087001593 roof hairpin; other site 159087001594 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 159087001595 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 159087001596 ring oligomerisation interface [polypeptide binding]; other site 159087001597 ATP/Mg binding site [chemical binding]; other site 159087001598 stacking interactions; other site 159087001599 hinge regions; other site 159087001600 Protein of unknown function, DUF485; Region: DUF485; pfam04341 159087001601 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 159087001602 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 159087001603 Na binding site [ion binding]; other site 159087001604 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087001605 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 159087001606 active site 159087001607 phosphorylation site [posttranslational modification] 159087001608 intermolecular recognition site; other site 159087001609 dimerization interface [polypeptide binding]; other site 159087001610 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 159087001611 DNA binding site [nucleotide binding] 159087001612 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 159087001613 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 159087001614 HAMP domain; Region: HAMP; pfam00672 159087001615 dimerization interface [polypeptide binding]; other site 159087001616 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 159087001617 dimer interface [polypeptide binding]; other site 159087001618 phosphorylation site [posttranslational modification] 159087001619 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 159087001620 ATP binding site [chemical binding]; other site 159087001621 Mg2+ binding site [ion binding]; other site 159087001622 G-X-G motif; other site 159087001623 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 159087001624 S-adenosylmethionine binding site [chemical binding]; other site 159087001625 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 159087001626 catalytic core [active] 159087001627 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 159087001628 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 159087001629 CoenzymeA binding site [chemical binding]; other site 159087001630 subunit interaction site [polypeptide binding]; other site 159087001631 PHB binding site; other site 159087001632 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 159087001633 FHA domain; Region: FHA; pfam00498 159087001634 phosphopeptide binding site; other site 159087001635 Protein phosphatase 2C; Region: PP2C; pfam00481 159087001636 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087001637 active site 159087001638 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087001639 Catalytic domain of Protein Kinases; Region: PKc; cd00180 159087001640 active site 159087001641 ATP binding site [chemical binding]; other site 159087001642 substrate binding site [chemical binding]; other site 159087001643 activation loop (A-loop); other site 159087001644 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 159087001645 PEGA domain; Region: PEGA; pfam08308 159087001646 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 159087001647 E3 interaction surface; other site 159087001648 lipoyl attachment site [posttranslational modification]; other site 159087001649 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 159087001650 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 159087001651 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 159087001652 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 159087001653 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 159087001654 E3 interaction surface; other site 159087001655 lipoyl attachment site [posttranslational modification]; other site 159087001656 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 159087001657 E3 interaction surface; other site 159087001658 lipoyl attachment site [posttranslational modification]; other site 159087001659 e3 binding domain; Region: E3_binding; pfam02817 159087001660 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 159087001661 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 159087001662 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 159087001663 dimer interface [polypeptide binding]; other site 159087001664 TPP-binding site [chemical binding]; other site 159087001665 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 159087001666 Subunit I/III interface [polypeptide binding]; other site 159087001667 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 159087001668 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 159087001669 dimer interface [polypeptide binding]; other site 159087001670 PYR/PP interface [polypeptide binding]; other site 159087001671 TPP binding site [chemical binding]; other site 159087001672 substrate binding site [chemical binding]; other site 159087001673 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 159087001674 TPP-binding site; other site 159087001675 indolepyruvate oxidoreductase subunit beta; Reviewed; Region: PRK06853 159087001676 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 159087001677 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 159087001678 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 159087001679 homodimer interface [polypeptide binding]; other site 159087001680 NADP binding site [chemical binding]; other site 159087001681 substrate binding site [chemical binding]; other site 159087001682 AIR carboxylase; Region: AIRC; pfam00731 159087001683 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 159087001684 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 159087001685 ATP-grasp domain; Region: ATP-grasp; pfam02222 159087001686 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 159087001687 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 159087001688 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 159087001689 aromatic arch; other site 159087001690 DCoH dimer interaction site [polypeptide binding]; other site 159087001691 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 159087001692 DCoH tetramer interaction site [polypeptide binding]; other site 159087001693 substrate binding site [chemical binding]; other site 159087001694 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 159087001695 PAS fold; Region: PAS_4; pfam08448 159087001696 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 159087001697 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 159087001698 Walker A motif; other site 159087001699 ATP binding site [chemical binding]; other site 159087001700 Walker B motif; other site 159087001701 arginine finger; other site 159087001702 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087001703 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 159087001704 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 159087001705 Coenzyme A transferase; Region: CoA_trans; smart00882 159087001706 Coenzyme A transferase; Region: CoA_trans; cl17247 159087001707 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087001708 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087001709 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 159087001710 Protein export membrane protein; Region: SecD_SecF; cl14618 159087001711 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087001712 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 159087001713 dimer interface [polypeptide binding]; other site 159087001714 phosphorylation site [posttranslational modification] 159087001715 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 159087001716 ATP binding site [chemical binding]; other site 159087001717 Mg2+ binding site [ion binding]; other site 159087001718 G-X-G motif; other site 159087001719 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087001720 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 159087001721 active site 159087001722 phosphorylation site [posttranslational modification] 159087001723 intermolecular recognition site; other site 159087001724 dimerization interface [polypeptide binding]; other site 159087001725 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 159087001726 Family of unknown function (DUF490); Region: DUF490; pfam04357 159087001727 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 159087001728 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 159087001729 Surface antigen; Region: Bac_surface_Ag; pfam01103 159087001730 Site-specific recombinase; Region: SpecificRecomb; pfam10136 159087001731 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087001732 ligand binding site [chemical binding]; other site 159087001733 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 159087001734 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 159087001735 nucleophile elbow; other site 159087001736 Surface antigen; Region: Bac_surface_Ag; pfam01103 159087001737 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 159087001738 Helix-hairpin-helix motif; Region: HHH; pfam00633 159087001739 probable DNA repair protein; Region: TIGR03623 159087001740 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 159087001741 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 159087001742 Part of AAA domain; Region: AAA_19; pfam13245 159087001743 Family description; Region: UvrD_C_2; pfam13538 159087001744 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 159087001745 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 159087001746 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 159087001747 substrate binding pocket [chemical binding]; other site 159087001748 membrane-bound complex binding site; other site 159087001749 hinge residues; other site 159087001750 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087001751 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087001752 metal binding site [ion binding]; metal-binding site 159087001753 active site 159087001754 I-site; other site 159087001755 putative metal dependent hydrolase; Provisional; Region: PRK11598 159087001756 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 159087001757 Sulfatase; Region: Sulfatase; pfam00884 159087001758 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 159087001759 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 159087001760 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 159087001761 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 159087001762 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 159087001763 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 159087001764 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087001765 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087001766 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 159087001767 dimerization interface [polypeptide binding]; other site 159087001768 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087001769 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 159087001770 active site 159087001771 phosphorylation site [posttranslational modification] 159087001772 intermolecular recognition site; other site 159087001773 dimerization interface [polypeptide binding]; other site 159087001774 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 159087001775 Walker A motif; other site 159087001776 ATP binding site [chemical binding]; other site 159087001777 Walker B motif; other site 159087001778 arginine finger; other site 159087001779 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087001780 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 159087001781 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 159087001782 dimer interface [polypeptide binding]; other site 159087001783 phosphorylation site [posttranslational modification] 159087001784 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 159087001785 ATP binding site [chemical binding]; other site 159087001786 Mg2+ binding site [ion binding]; other site 159087001787 G-X-G motif; other site 159087001788 hypothetical protein; Provisional; Region: PRK10621 159087001789 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087001790 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 159087001791 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 159087001792 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 159087001793 Aspartase; Region: Aspartase; cd01357 159087001794 active sites [active] 159087001795 tetramer interface [polypeptide binding]; other site 159087001796 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 159087001797 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087001798 putative substrate translocation pore; other site 159087001799 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 159087001800 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 159087001801 dimer interface [polypeptide binding]; other site 159087001802 ssDNA binding site [nucleotide binding]; other site 159087001803 tetramer (dimer of dimers) interface [polypeptide binding]; other site 159087001804 HDOD domain; Region: HDOD; pfam08668 159087001805 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 159087001806 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 159087001807 potassium uptake protein; Region: kup; TIGR00794 159087001808 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 159087001809 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 159087001810 active site 159087001811 HIGH motif; other site 159087001812 nucleotide binding site [chemical binding]; other site 159087001813 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 159087001814 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 159087001815 DNA binding residues [nucleotide binding] 159087001816 B12 binding domain; Region: B12-binding_2; pfam02607 159087001817 B12 binding domain; Region: B12-binding; pfam02310 159087001818 B12 binding site [chemical binding]; other site 159087001819 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 159087001820 catalytic residues [active] 159087001821 dimer interface [polypeptide binding]; other site 159087001822 putative GTP cyclohydrolase; Provisional; Region: PRK13674 159087001823 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 159087001824 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 159087001825 hydroxyglutarate oxidase; Provisional; Region: PRK11728 159087001826 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 159087001827 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 159087001828 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 159087001829 S-adenosylmethionine binding site [chemical binding]; other site 159087001830 MFS/sugar transport protein; Region: MFS_2; pfam13347 159087001831 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 159087001832 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087001833 NAD(P) binding site [chemical binding]; other site 159087001834 active site 159087001835 SnoaL-like domain; Region: SnoaL_2; pfam12680 159087001836 Ion channel; Region: Ion_trans_2; pfam07885 159087001837 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 159087001838 TrkA-N domain; Region: TrkA_N; pfam02254 159087001839 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 159087001840 TrkA-N domain; Region: TrkA_N; pfam02254 159087001841 outer membrane lipoprotein; Provisional; Region: PRK11023 159087001842 BON domain; Region: BON; pfam04972 159087001843 BON domain; Region: BON; pfam04972 159087001844 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 159087001845 dimer interface [polypeptide binding]; other site 159087001846 active site 159087001847 The HIRAN protein (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p; Region: HIRAN; smart00910 159087001848 hypothetical protein; Provisional; Region: PRK14673 159087001849 Predicted methyltransferases [General function prediction only]; Region: COG0313 159087001850 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 159087001851 putative SAM binding site [chemical binding]; other site 159087001852 putative homodimer interface [polypeptide binding]; other site 159087001853 PAS fold; Region: PAS_4; pfam08448 159087001854 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 159087001855 putative active site [active] 159087001856 heme pocket [chemical binding]; other site 159087001857 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 159087001858 PAS domain; Region: PAS_9; pfam13426 159087001859 putative active site [active] 159087001860 heme pocket [chemical binding]; other site 159087001861 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087001862 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087001863 metal binding site [ion binding]; metal-binding site 159087001864 active site 159087001865 I-site; other site 159087001866 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 159087001867 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 159087001868 active site 159087001869 substrate binding pocket [chemical binding]; other site 159087001870 dimer interface [polypeptide binding]; other site 159087001871 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 159087001872 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 159087001873 rRNA binding site [nucleotide binding]; other site 159087001874 predicted 30S ribosome binding site; other site 159087001875 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 159087001876 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 159087001877 2-isopropylmalate synthase; Validated; Region: PRK03739 159087001878 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 159087001879 active site 159087001880 catalytic residues [active] 159087001881 metal binding site [ion binding]; metal-binding site 159087001882 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 159087001883 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 159087001884 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 159087001885 putative DNA binding site [nucleotide binding]; other site 159087001886 putative Zn2+ binding site [ion binding]; other site 159087001887 AsnC family; Region: AsnC_trans_reg; pfam01037 159087001888 Putative methyltransferase; Region: Methyltransf_16; pfam10294 159087001889 thiopurine S-methyltransferase; Reviewed; Region: PRK13255 159087001890 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 159087001891 S-adenosylmethionine binding site [chemical binding]; other site 159087001892 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 159087001893 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 159087001894 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 159087001895 Walker A motif; other site 159087001896 ATP binding site [chemical binding]; other site 159087001897 Walker B motif; other site 159087001898 arginine finger; other site 159087001899 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 159087001900 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 159087001901 S-adenosylmethionine binding site [chemical binding]; other site 159087001902 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 159087001903 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 159087001904 RNA polymerase sigma factor; Provisional; Region: PRK12511 159087001905 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087001906 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 159087001907 DNA binding residues [nucleotide binding] 159087001908 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 159087001909 Putative zinc-finger; Region: zf-HC2; pfam13490 159087001910 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 159087001911 putative heme binding pocket [chemical binding]; other site 159087001912 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087001913 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087001914 putative ligand binding site [chemical binding]; other site 159087001915 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 159087001916 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 159087001917 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 159087001918 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 159087001919 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087001920 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 159087001921 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 159087001922 DNA binding residues [nucleotide binding] 159087001923 DNA primase; Validated; Region: dnaG; PRK05667 159087001924 CHC2 zinc finger; Region: zf-CHC2; pfam01807 159087001925 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 159087001926 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 159087001927 active site 159087001928 metal binding site [ion binding]; metal-binding site 159087001929 interdomain interaction site; other site 159087001930 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 159087001931 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 159087001932 Yqey-like protein; Region: YqeY; pfam09424 159087001933 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 159087001934 UGMP family protein; Validated; Region: PRK09604 159087001935 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 159087001936 Cupin domain; Region: Cupin_2; cl17218 159087001937 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 159087001938 dimer interface [polypeptide binding]; other site 159087001939 catalytic triad [active] 159087001940 peroxidatic and resolving cysteines [active] 159087001941 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 159087001942 Dihydroneopterin aldolase; Region: FolB; smart00905 159087001943 active site 159087001944 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 159087001945 putative deacylase active site [active] 159087001946 hypothetical protein; Provisional; Region: PRK09256 159087001947 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 159087001948 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 159087001949 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 159087001950 active site 159087001951 Int/Topo IB signature motif; other site 159087001952 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 159087001953 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 159087001954 DNA binding site [nucleotide binding] 159087001955 active site 159087001956 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 159087001957 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 159087001958 FAD binding site [chemical binding]; other site 159087001959 substrate binding pocket [chemical binding]; other site 159087001960 catalytic base [active] 159087001961 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 159087001962 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 159087001963 putative catalytic cysteine [active] 159087001964 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 159087001965 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 159087001966 Lipopolysaccharide-assembly; Region: LptE; pfam04390 159087001967 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 159087001968 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 159087001969 HIGH motif; other site 159087001970 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 159087001971 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087001972 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087001973 active site 159087001974 KMSKS motif; other site 159087001975 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 159087001976 tRNA binding surface [nucleotide binding]; other site 159087001977 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 159087001978 Part of AAA domain; Region: AAA_19; pfam13245 159087001979 Family description; Region: UvrD_C_2; pfam13538 159087001980 Uncharacterized conserved protein [Function unknown]; Region: COG1434 159087001981 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 159087001982 putative active site [active] 159087001983 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 159087001984 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 159087001985 NADP binding site [chemical binding]; other site 159087001986 dimer interface [polypeptide binding]; other site 159087001987 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 159087001988 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 159087001989 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 159087001990 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 159087001991 P-loop; other site 159087001992 Magnesium ion binding site [ion binding]; other site 159087001993 CHASE domain; Region: CHASE; pfam03924 159087001994 PAS fold; Region: PAS_4; pfam08448 159087001995 PAS domain S-box; Region: sensory_box; TIGR00229 159087001996 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 159087001997 putative active site [active] 159087001998 heme pocket [chemical binding]; other site 159087001999 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087002000 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 159087002001 dimer interface [polypeptide binding]; other site 159087002002 phosphorylation site [posttranslational modification] 159087002003 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 159087002004 ATP binding site [chemical binding]; other site 159087002005 G-X-G motif; other site 159087002006 Response regulator receiver domain; Region: Response_reg; pfam00072 159087002007 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 159087002008 active site 159087002009 phosphorylation site [posttranslational modification] 159087002010 intermolecular recognition site; other site 159087002011 dimerization interface [polypeptide binding]; other site 159087002012 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087002013 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 159087002014 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 159087002015 putative dimerization interface [polypeptide binding]; other site 159087002016 Pirin-related protein [General function prediction only]; Region: COG1741 159087002017 Pirin; Region: Pirin; pfam02678 159087002018 Flavodoxin domain; Region: Flavodoxin_5; cl17428 159087002019 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 159087002020 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 159087002021 Response regulator receiver domain; Region: Response_reg; pfam00072 159087002022 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 159087002023 active site 159087002024 phosphorylation site [posttranslational modification] 159087002025 intermolecular recognition site; other site 159087002026 dimerization interface [polypeptide binding]; other site 159087002027 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 159087002028 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 159087002029 active site 159087002030 phosphorylation site [posttranslational modification] 159087002031 intermolecular recognition site; other site 159087002032 dimerization interface [polypeptide binding]; other site 159087002033 BNR repeat-like domain; Region: BNR_2; pfam13088 159087002034 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 159087002035 enoyl-CoA hydratase; Validated; Region: PRK08139 159087002036 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 159087002037 substrate binding site [chemical binding]; other site 159087002038 oxyanion hole (OAH) forming residues; other site 159087002039 trimer interface [polypeptide binding]; other site 159087002040 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 159087002041 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 159087002042 putative active site [active] 159087002043 putative PHP Thumb interface [polypeptide binding]; other site 159087002044 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 159087002045 generic binding surface II; other site 159087002046 generic binding surface I; other site 159087002047 cupin fold metalloprotein, WbuC family; Region: cupin_WbuC; TIGR04366 159087002048 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087002049 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087002050 dimer interface [polypeptide binding]; other site 159087002051 putative CheW interface [polypeptide binding]; other site 159087002052 Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Region: HTH_MerR-trunc; cd04762 159087002053 DNA binding residues [nucleotide binding] 159087002054 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087002055 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 159087002056 active site 159087002057 phosphorylation site [posttranslational modification] 159087002058 intermolecular recognition site; other site 159087002059 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 159087002060 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 159087002061 dimer interface [polypeptide binding]; other site 159087002062 decamer (pentamer of dimers) interface [polypeptide binding]; other site 159087002063 catalytic triad [active] 159087002064 peroxidatic and resolving cysteines [active] 159087002065 NADH:ubiquinone oxidoreductase subunit 4 (chain M) [Energy production and conversion]; Region: NuoM; COG1008 159087002066 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 159087002067 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 159087002068 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 159087002069 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 159087002070 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 159087002071 proton-translocating NADH-quinone oxidoreductase, chain M; Region: NDH_I_M; TIGR01972 159087002072 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 159087002073 NADH:ubiquinone oxidoreductase subunit 4 (chain M) [Energy production and conversion]; Region: NuoM; COG1008 159087002074 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 159087002075 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 159087002076 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 159087002077 PhnA protein; Region: PhnA; pfam03831 159087002078 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 159087002079 putative transporter; Provisional; Region: PRK11660 159087002080 Sulfate transporter family; Region: Sulfate_transp; pfam00916 159087002081 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 159087002082 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 159087002083 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 159087002084 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 159087002085 active site 159087002086 HIGH motif; other site 159087002087 KMSKS motif; other site 159087002088 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 159087002089 tRNA binding surface [nucleotide binding]; other site 159087002090 anticodon binding site; other site 159087002091 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 159087002092 dimer interface [polypeptide binding]; other site 159087002093 putative tRNA-binding site [nucleotide binding]; other site 159087002094 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087002095 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 159087002096 active site 159087002097 phosphorylation site [posttranslational modification] 159087002098 intermolecular recognition site; other site 159087002099 dimerization interface [polypeptide binding]; other site 159087002100 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 159087002101 DNA binding site [nucleotide binding] 159087002102 Domain of unknown function DUF59; Region: DUF59; pfam01883 159087002103 antiporter inner membrane protein; Provisional; Region: PRK11670 159087002104 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 159087002105 Walker A motif; other site 159087002106 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 159087002107 trimer interface [polypeptide binding]; other site 159087002108 active site 159087002109 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 159087002110 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 159087002111 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 159087002112 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087002113 catalytic residue [active] 159087002114 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 159087002115 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 159087002116 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 159087002117 folate binding site [chemical binding]; other site 159087002118 NADP+ binding site [chemical binding]; other site 159087002119 glycogen synthase; Provisional; Region: glgA; PRK00654 159087002120 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 159087002121 ADP-binding pocket [chemical binding]; other site 159087002122 homodimer interface [polypeptide binding]; other site 159087002123 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 159087002124 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 159087002125 active site 159087002126 dimer interface [polypeptide binding]; other site 159087002127 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 159087002128 dimer interface [polypeptide binding]; other site 159087002129 active site 159087002130 This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important...; Region: GT1_Glycogen_Phosphorylase_like; cd04299 159087002131 putative homodimer interface [polypeptide binding]; other site 159087002132 putative active site pocket [active] 159087002133 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 159087002134 N-terminal catalytic domain of 4-alpha-glucanotransferase; glycoside hydrolase family 57 (GH57); Region: GH57N_TLGT_like; cd10793 159087002135 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 159087002136 active site 159087002137 catalytic site [active] 159087002138 homodimer interface [polypeptide binding]; other site 159087002139 Lid 1; other site 159087002140 Domain of unknown function (DUF1925); Region: DUF1925; pfam09094 159087002141 Domain of unknown function (DUF1926); Region: DUF1926; pfam09095 159087002142 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 159087002143 N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57); Region: GH57N_APU; cd10796 159087002144 putative active site [active] 159087002145 catalytic site [active] 159087002146 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 159087002147 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 159087002148 ligand binding site; other site 159087002149 oligomer interface; other site 159087002150 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 159087002151 dimer interface [polypeptide binding]; other site 159087002152 N-terminal domain interface [polypeptide binding]; other site 159087002153 sulfate 1 binding site; other site 159087002154 glycogen branching enzyme; Provisional; Region: PRK12313 159087002155 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 159087002156 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 159087002157 active site 159087002158 catalytic site [active] 159087002159 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 159087002160 Protein of unknown function (DUF1345); Region: DUF1345; pfam07077 159087002161 glucokinase, proteobacterial type; Region: glk; TIGR00749 159087002162 Glucokinase; Region: Glucokinase; pfam02685 159087002163 thymidylate synthase; Reviewed; Region: thyA; PRK01827 159087002164 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 159087002165 dimerization interface [polypeptide binding]; other site 159087002166 active site 159087002167 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 159087002168 MPT binding site; other site 159087002169 trimer interface [polypeptide binding]; other site 159087002170 hypothetical protein; Provisional; Region: PRK05255 159087002171 peptidase PmbA; Provisional; Region: PRK11040 159087002172 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 159087002173 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 159087002174 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 159087002175 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 159087002176 dimerization interface [polypeptide binding]; other site 159087002177 DPS ferroxidase diiron center [ion binding]; other site 159087002178 ion pore; other site 159087002179 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 159087002180 DctM-like transporters; Region: DctM; pfam06808 159087002181 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 159087002182 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 159087002183 catalytic core [active] 159087002184 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 159087002185 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 159087002186 dimer interface [polypeptide binding]; other site 159087002187 active site 159087002188 glycine-pyridoxal phosphate binding site [chemical binding]; other site 159087002189 folate binding site [chemical binding]; other site 159087002190 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 159087002191 ATP cone domain; Region: ATP-cone; pfam03477 159087002192 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 159087002193 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 159087002194 catalytic motif [active] 159087002195 Zn binding site [ion binding]; other site 159087002196 RibD C-terminal domain; Region: RibD_C; cl17279 159087002197 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 159087002198 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 159087002199 ATP binding site [chemical binding]; other site 159087002200 substrate interface [chemical binding]; other site 159087002201 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 159087002202 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 159087002203 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 159087002204 protein binding site [polypeptide binding]; other site 159087002205 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 159087002206 Catalytic dyad [active] 159087002207 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 159087002208 Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Region: Cenp-F_leu_zip; pfam10473 159087002209 Peptidase family M23; Region: Peptidase_M23; pfam01551 159087002210 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 159087002211 dimerization interface [polypeptide binding]; other site 159087002212 putative DNA binding site [nucleotide binding]; other site 159087002213 putative Zn2+ binding site [ion binding]; other site 159087002214 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 159087002215 active site residue [active] 159087002216 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 159087002217 GSH binding site [chemical binding]; other site 159087002218 catalytic residues [active] 159087002219 preprotein translocase subunit SecB; Validated; Region: PRK05751 159087002220 SecA binding site; other site 159087002221 Preprotein binding site; other site 159087002222 Bacterial SH3 domain; Region: SH3_4; pfam06347 159087002223 Bacterial SH3 domain; Region: SH3_4; pfam06347 159087002224 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 159087002225 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 159087002226 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 159087002227 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 159087002228 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 159087002229 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 159087002230 active site 159087002231 biotin synthase; Region: bioB; TIGR00433 159087002232 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 159087002233 FeS/SAM binding site; other site 159087002234 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 159087002235 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 159087002236 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 159087002237 S-adenosylmethionine binding site [chemical binding]; other site 159087002238 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 159087002239 TMAO/DMSO reductase; Reviewed; Region: PRK05363 159087002240 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 159087002241 Moco binding site; other site 159087002242 metal coordination site [ion binding]; other site 159087002243 HDOD domain; Region: HDOD; pfam08668 159087002244 HD domain; Region: HD; pfam01966 159087002245 FOG: CBS domain [General function prediction only]; Region: COG0517 159087002246 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 159087002247 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087002248 Cytochrome c553 [Energy production and conversion]; Region: COG2863 159087002249 Cytochrome c; Region: Cytochrom_C; cl11414 159087002250 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 159087002251 G1 box; other site 159087002252 GTP/Mg2+ binding site [chemical binding]; other site 159087002253 Switch I region; other site 159087002254 G2 box; other site 159087002255 G3 box; other site 159087002256 Switch II region; other site 159087002257 G4 box; other site 159087002258 G5 box; other site 159087002259 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 159087002260 dimer interface [polypeptide binding]; other site 159087002261 active site 159087002262 aspartate-rich active site metal binding site; other site 159087002263 allosteric magnesium binding site [ion binding]; other site 159087002264 Schiff base residues; other site 159087002265 division inhibitor protein; Provisional; Region: slmA; PRK09480 159087002266 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087002267 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 159087002268 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 159087002269 motif II; other site 159087002270 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 159087002271 feedback inhibition sensing region; other site 159087002272 homohexameric interface [polypeptide binding]; other site 159087002273 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 159087002274 nucleotide binding site [chemical binding]; other site 159087002275 N-acetyl-L-glutamate binding site [chemical binding]; other site 159087002276 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 159087002277 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 159087002278 putative dimer interface [polypeptide binding]; other site 159087002279 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_7; cd04664 159087002280 nudix motif; other site 159087002281 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 159087002282 putative RNAase interaction site [polypeptide binding]; other site 159087002283 RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate...; Region: RNase_Sa; cd00607 159087002284 active site 159087002285 barstar interaction site; other site 159087002286 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 159087002287 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 159087002288 dimer interface [polypeptide binding]; other site 159087002289 anticodon binding site; other site 159087002290 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 159087002291 homodimer interface [polypeptide binding]; other site 159087002292 motif 1; other site 159087002293 active site 159087002294 motif 2; other site 159087002295 GAD domain; Region: GAD; pfam02938 159087002296 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 159087002297 motif 3; other site 159087002298 Uncharacterized conserved protein [Function unknown]; Region: COG2928 159087002299 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 159087002300 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 159087002301 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 159087002302 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 159087002303 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 159087002304 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 159087002305 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 159087002306 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 159087002307 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 159087002308 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 159087002309 Walker A motif; other site 159087002310 ATP binding site [chemical binding]; other site 159087002311 Walker B motif; other site 159087002312 Domain of unknown function DUF21; Region: DUF21; pfam01595 159087002313 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 159087002314 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 159087002315 Transporter associated domain; Region: CorC_HlyC; smart01091 159087002316 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 159087002317 signal recognition particle protein; Provisional; Region: PRK10867 159087002318 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 159087002319 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 159087002320 P loop; other site 159087002321 GTP binding site [chemical binding]; other site 159087002322 Signal peptide binding domain; Region: SRP_SPB; pfam02978 159087002323 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 159087002324 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 159087002325 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087002326 catalytic residue [active] 159087002327 prolyl-tRNA synthetase; Provisional; Region: PRK09194 159087002328 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 159087002329 dimer interface [polypeptide binding]; other site 159087002330 motif 1; other site 159087002331 active site 159087002332 motif 2; other site 159087002333 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 159087002334 putative deacylase active site [active] 159087002335 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 159087002336 active site 159087002337 motif 3; other site 159087002338 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 159087002339 anticodon binding site; other site 159087002340 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 159087002341 putative active site [active] 159087002342 Ap4A binding site [chemical binding]; other site 159087002343 nudix motif; other site 159087002344 putative metal binding site [ion binding]; other site 159087002345 CNP1-like family; Region: CNP1; pfam08750 159087002346 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 159087002347 diiron binding motif [ion binding]; other site 159087002348 OsmC-like protein; Region: OsmC; cl00767 159087002349 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 159087002350 23S rRNA interface [nucleotide binding]; other site 159087002351 L3 interface [polypeptide binding]; other site 159087002352 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 159087002353 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 159087002354 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 159087002355 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087002356 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 159087002357 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 159087002358 putative ATP binding site [chemical binding]; other site 159087002359 putative substrate interface [chemical binding]; other site 159087002360 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 159087002361 putative binding surface; other site 159087002362 active site 159087002363 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087002364 Zn2+ binding site [ion binding]; other site 159087002365 Mg2+ binding site [ion binding]; other site 159087002366 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 159087002367 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 159087002368 substrate binding pocket [chemical binding]; other site 159087002369 chain length determination region; other site 159087002370 substrate-Mg2+ binding site; other site 159087002371 catalytic residues [active] 159087002372 aspartate-rich region 1; other site 159087002373 active site lid residues [active] 159087002374 aspartate-rich region 2; other site 159087002375 Protein of unknown function (DUF3553); Region: DUF3553; pfam12073 159087002376 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087002377 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 159087002378 dimer interface [polypeptide binding]; other site 159087002379 phosphorylation site [posttranslational modification] 159087002380 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 159087002381 ATP binding site [chemical binding]; other site 159087002382 Mg2+ binding site [ion binding]; other site 159087002383 G-X-G motif; other site 159087002384 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087002385 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 159087002386 active site 159087002387 phosphorylation site [posttranslational modification] 159087002388 intermolecular recognition site; other site 159087002389 dimerization interface [polypeptide binding]; other site 159087002390 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 159087002391 Walker A motif; other site 159087002392 ATP binding site [chemical binding]; other site 159087002393 Walker B motif; other site 159087002394 arginine finger; other site 159087002395 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087002396 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 159087002397 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 159087002398 amidase catalytic site [active] 159087002399 Zn binding residues [ion binding]; other site 159087002400 substrate binding site [chemical binding]; other site 159087002401 hypothetical protein; Provisional; Region: PRK08960 159087002402 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 159087002403 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087002404 homodimer interface [polypeptide binding]; other site 159087002405 catalytic residue [active] 159087002406 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_GTP; cd00819 159087002407 active site 159087002408 substrate-binding site [chemical binding]; other site 159087002409 metal-binding site [ion binding] 159087002410 GTP binding site [chemical binding]; other site 159087002411 malic enzyme; Reviewed; Region: PRK12862 159087002412 Malic enzyme, N-terminal domain; Region: malic; pfam00390 159087002413 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 159087002414 putative NAD(P) binding site [chemical binding]; other site 159087002415 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 159087002416 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 159087002417 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 159087002418 Transcriptional regulator [Transcription]; Region: IclR; COG1414 159087002419 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 159087002420 Bacterial transcriptional regulator; Region: IclR; pfam01614 159087002421 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 159087002422 Cysteine-rich domain; Region: CCG; pfam02754 159087002423 Cysteine-rich domain; Region: CCG; pfam02754 159087002424 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 159087002425 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 159087002426 4Fe-4S binding domain; Region: Fer4; pfam00037 159087002427 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 159087002428 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 159087002429 NAD(P) binding site [chemical binding]; other site 159087002430 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 159087002431 glycerate dehydrogenase; Provisional; Region: PRK06487 159087002432 putative ligand binding site [chemical binding]; other site 159087002433 putative NAD binding site [chemical binding]; other site 159087002434 catalytic site [active] 159087002435 Uncharacterized conserved protein [Function unknown]; Region: COG1556 159087002436 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 159087002437 PAS domain; Region: PAS_9; pfam13426 159087002438 putative active site [active] 159087002439 heme pocket [chemical binding]; other site 159087002440 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087002441 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087002442 dimer interface [polypeptide binding]; other site 159087002443 putative CheW interface [polypeptide binding]; other site 159087002444 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087002445 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 159087002446 putative active site [active] 159087002447 heme pocket [chemical binding]; other site 159087002448 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 159087002449 putative active site [active] 159087002450 heme pocket [chemical binding]; other site 159087002451 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 159087002452 PAS domain; Region: PAS_9; pfam13426 159087002453 putative active site [active] 159087002454 heme pocket [chemical binding]; other site 159087002455 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087002456 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087002457 metal binding site [ion binding]; metal-binding site 159087002458 active site 159087002459 I-site; other site 159087002460 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 159087002461 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 159087002462 RNA binding surface [nucleotide binding]; other site 159087002463 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 159087002464 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 159087002465 putative acyl-acceptor binding pocket; other site 159087002466 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 159087002467 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 159087002468 Phosphate transporter family; Region: PHO4; pfam01384 159087002469 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 159087002470 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_like_3; cd09321 159087002471 gating phenylalanine in ion channel; other site 159087002472 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087002473 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087002474 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 159087002475 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 159087002476 PAS fold; Region: PAS_4; pfam08448 159087002477 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 159087002478 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 159087002479 Walker A motif; other site 159087002480 ATP binding site [chemical binding]; other site 159087002481 Walker B motif; other site 159087002482 arginine finger; other site 159087002483 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 159087002484 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 159087002485 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 159087002486 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 159087002487 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 159087002488 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 159087002489 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 159087002490 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 159087002491 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 159087002492 MASE1; Region: MASE1; cl17823 159087002493 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 159087002494 ATP binding site [chemical binding]; other site 159087002495 Mg2+ binding site [ion binding]; other site 159087002496 G-X-G motif; other site 159087002497 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087002498 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 159087002499 active site 159087002500 phosphorylation site [posttranslational modification] 159087002501 intermolecular recognition site; other site 159087002502 dimerization interface [polypeptide binding]; other site 159087002503 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 159087002504 DNA binding residues [nucleotide binding] 159087002505 dimerization interface [polypeptide binding]; other site 159087002506 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 159087002507 dimerization interface [polypeptide binding]; other site 159087002508 putative DNA binding site [nucleotide binding]; other site 159087002509 putative Zn2+ binding site [ion binding]; other site 159087002510 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09560 159087002511 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 159087002512 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 159087002513 putative active site [active] 159087002514 putative NTP binding site [chemical binding]; other site 159087002515 putative nucleic acid binding site [nucleotide binding]; other site 159087002516 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 159087002517 Cytochrome c; Region: Cytochrom_C; cl11414 159087002518 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087002519 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087002520 ligand binding site [chemical binding]; other site 159087002521 Transcriptional regulators [Transcription]; Region: MarR; COG1846 159087002522 MarR family; Region: MarR_2; pfam12802 159087002523 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087002524 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087002525 ligand binding site [chemical binding]; other site 159087002526 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 159087002527 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 159087002528 putative ion selectivity filter; other site 159087002529 putative pore gating glutamate residue; other site 159087002530 putative H+/Cl- coupling transport residue; other site 159087002531 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 159087002532 putative DNA binding site [nucleotide binding]; other site 159087002533 putative Zn2+ binding site [ion binding]; other site 159087002534 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 159087002535 Low molecular weight phosphatase family; Region: LMWPc; cd00115 159087002536 active site 159087002537 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 159087002538 arsenical-resistance protein; Region: acr3; TIGR00832 159087002539 Predicted permease; Region: DUF318; cl17795 159087002540 Predicted permease; Region: DUF318; cl17795 159087002541 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 159087002542 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]; Region: FRQ1; COG5126 159087002543 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087002544 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 159087002545 active site 159087002546 phosphorylation site [posttranslational modification] 159087002547 intermolecular recognition site; other site 159087002548 dimerization interface [polypeptide binding]; other site 159087002549 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 159087002550 DNA binding site [nucleotide binding] 159087002551 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087002552 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 159087002553 dimerization interface [polypeptide binding]; other site 159087002554 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 159087002555 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 159087002556 dimer interface [polypeptide binding]; other site 159087002557 phosphorylation site [posttranslational modification] 159087002558 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 159087002559 ATP binding site [chemical binding]; other site 159087002560 Mg2+ binding site [ion binding]; other site 159087002561 G-X-G motif; other site 159087002562 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 159087002563 SnoaL-like domain; Region: SnoaL_2; pfam12680 159087002564 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 159087002565 substrate binding site [chemical binding]; other site 159087002566 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 159087002567 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 159087002568 Response regulator receiver domain; Region: Response_reg; pfam00072 159087002569 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 159087002570 active site 159087002571 phosphorylation site [posttranslational modification] 159087002572 intermolecular recognition site; other site 159087002573 dimerization interface [polypeptide binding]; other site 159087002574 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087002575 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087002576 metal binding site [ion binding]; metal-binding site 159087002577 active site 159087002578 I-site; other site 159087002579 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 159087002580 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 159087002581 NAD binding site [chemical binding]; other site 159087002582 homodimer interface [polypeptide binding]; other site 159087002583 homotetramer interface [polypeptide binding]; other site 159087002584 active site 159087002585 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 159087002586 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087002587 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 159087002588 metal-binding site [ion binding] 159087002589 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087002590 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 159087002591 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 159087002592 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 159087002593 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 159087002594 Low-spin heme binding site [chemical binding]; other site 159087002595 Putative water exit pathway; other site 159087002596 Binuclear center (active site) [active] 159087002597 Putative proton exit pathway; other site 159087002598 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 159087002599 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 159087002600 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 159087002601 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 159087002602 Cytochrome c; Region: Cytochrom_C; pfam00034 159087002603 Cytochrome c; Region: Cytochrom_C; pfam00034 159087002604 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087002605 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087002606 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 159087002607 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 159087002608 FixH; Region: FixH; pfam05751 159087002609 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 159087002610 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 159087002611 nudix motif; other site 159087002612 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 159087002613 flagellar motor stator protein MotA; Region: MotA1; TIGR03818 159087002614 flagellar motor protein MotB; Validated; Region: motB; PRK09041 159087002615 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 159087002616 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087002617 ligand binding site [chemical binding]; other site 159087002618 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087002619 Response regulator receiver domain; Region: Response_reg; pfam00072 159087002620 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 159087002621 active site 159087002622 phosphorylation site [posttranslational modification] 159087002623 intermolecular recognition site; other site 159087002624 dimerization interface [polypeptide binding]; other site 159087002625 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 159087002626 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 159087002627 putative binding surface; other site 159087002628 active site 159087002629 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 159087002630 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 159087002631 ATP binding site [chemical binding]; other site 159087002632 Mg2+ binding site [ion binding]; other site 159087002633 G-X-G motif; other site 159087002634 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 159087002635 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 159087002636 putative CheA interaction surface; other site 159087002637 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 159087002638 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087002639 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 159087002640 dimerization interface [polypeptide binding]; other site 159087002641 PAS domain; Region: PAS_9; pfam13426 159087002642 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087002643 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087002644 dimer interface [polypeptide binding]; other site 159087002645 putative CheW interface [polypeptide binding]; other site 159087002646 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 159087002647 PAS domain; Region: PAS_9; pfam13426 159087002648 putative active site [active] 159087002649 heme pocket [chemical binding]; other site 159087002650 Tar ligand binding domain homologue; Region: TarH; pfam02203 159087002651 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087002652 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 159087002653 dimerization interface [polypeptide binding]; other site 159087002654 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087002655 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087002656 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087002657 dimer interface [polypeptide binding]; other site 159087002658 putative CheW interface [polypeptide binding]; other site 159087002659 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 159087002660 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 159087002661 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 159087002662 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 159087002663 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 159087002664 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 159087002665 active site 159087002666 phosphorylation site [posttranslational modification] 159087002667 intermolecular recognition site; other site 159087002668 dimerization interface [polypeptide binding]; other site 159087002669 CheB methylesterase; Region: CheB_methylest; pfam01339 159087002670 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 159087002671 anti sigma factor interaction site; other site 159087002672 regulatory phosphorylation site [posttranslational modification]; other site 159087002673 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 159087002674 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087002675 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 159087002676 active site 159087002677 phosphorylation site [posttranslational modification] 159087002678 intermolecular recognition site; other site 159087002679 dimerization interface [polypeptide binding]; other site 159087002680 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 159087002681 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087002682 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 159087002683 active site 159087002684 phosphorylation site [posttranslational modification] 159087002685 intermolecular recognition site; other site 159087002686 dimerization interface [polypeptide binding]; other site 159087002687 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 159087002688 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 159087002689 active site 159087002690 phosphorylation site [posttranslational modification] 159087002691 intermolecular recognition site; other site 159087002692 dimerization interface [polypeptide binding]; other site 159087002693 chemotaxis regulator CheZ; Provisional; Region: PRK11166 159087002694 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 159087002695 putative binding surface; other site 159087002696 active site 159087002697 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 159087002698 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 159087002699 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 159087002700 ATP binding site [chemical binding]; other site 159087002701 Mg2+ binding site [ion binding]; other site 159087002702 G-X-G motif; other site 159087002703 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087002704 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 159087002705 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 159087002706 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 159087002707 FHIPEP family; Region: FHIPEP; pfam00771 159087002708 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 159087002709 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 159087002710 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 159087002711 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 159087002712 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 159087002713 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 159087002714 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087002715 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 159087002716 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 159087002717 DNA binding residues [nucleotide binding] 159087002718 flagellar motor protein MotA; Validated; Region: PRK08124 159087002719 flagellar motor protein; Reviewed; Region: motC; PRK09109 159087002720 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 159087002721 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 159087002722 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087002723 ligand binding site [chemical binding]; other site 159087002724 FlgN protein; Region: FlgN; pfam05130 159087002725 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 159087002726 SAF-like; Region: SAF_2; pfam13144 159087002727 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 159087002728 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 159087002729 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 159087002730 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 159087002731 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 159087002732 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 159087002733 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 159087002734 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 159087002735 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 159087002736 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 159087002737 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 159087002738 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 159087002739 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 159087002740 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 159087002741 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 159087002742 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 159087002743 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 159087002744 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 159087002745 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 159087002746 Flagellar L-ring protein; Region: FlgH; pfam02107 159087002747 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 159087002748 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 159087002749 Rod binding protein; Region: Rod-binding; cl01626 159087002750 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 159087002751 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 159087002752 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 159087002753 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 159087002754 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 159087002755 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 159087002756 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 159087002757 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 159087002758 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 159087002759 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 159087002760 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 159087002761 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 159087002762 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 159087002763 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 159087002764 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 159087002765 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 159087002766 Flagellar FliJ protein; Region: FliJ; pfam02050 159087002767 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 159087002768 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 159087002769 Walker A motif/ATP binding site; other site 159087002770 Walker B motif; other site 159087002771 flagellar assembly protein H; Validated; Region: fliH; PRK05687 159087002772 Flagellar assembly protein FliH; Region: FliH; pfam02108 159087002773 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 159087002774 FliG C-terminal domain; Region: FliG_C; pfam01706 159087002775 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 159087002776 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 159087002777 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 159087002778 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 159087002779 dimer interface [polypeptide binding]; other site 159087002780 phosphorylation site [posttranslational modification] 159087002781 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 159087002782 ATP binding site [chemical binding]; other site 159087002783 Mg2+ binding site [ion binding]; other site 159087002784 G-X-G motif; other site 159087002785 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087002786 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 159087002787 active site 159087002788 phosphorylation site [posttranslational modification] 159087002789 intermolecular recognition site; other site 159087002790 dimerization interface [polypeptide binding]; other site 159087002791 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 159087002792 Walker A motif; other site 159087002793 ATP binding site [chemical binding]; other site 159087002794 Walker B motif; other site 159087002795 arginine finger; other site 159087002796 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087002797 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 159087002798 Flagellar regulator YcgR; Region: YcgR; pfam07317 159087002799 PilZ domain; Region: PilZ; pfam07238 159087002800 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 159087002801 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 159087002802 Flagellar protein FliT; Region: FliT; pfam05400 159087002803 Flagellar protein FliS; Region: FliS; cl00654 159087002804 flagellar capping protein; Reviewed; Region: fliD; PRK08032 159087002805 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 159087002806 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 159087002807 FlaG protein; Region: FlaG; pfam03646 159087002808 flagellin; Provisional; Region: PRK12802 159087002809 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 159087002810 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 159087002811 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 159087002812 binding surface 159087002813 Tetratricopeptide repeat; Region: TPR_16; pfam13432 159087002814 TPR motif; other site 159087002815 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 159087002816 TPR motif; other site 159087002817 binding surface 159087002818 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 159087002819 TPR motif; other site 159087002820 binding surface 159087002821 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 159087002822 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 159087002823 TPR motif; other site 159087002824 TPR repeat; Region: TPR_11; pfam13414 159087002825 binding surface 159087002826 Methyltransferase domain; Region: Methyltransf_23; pfam13489 159087002827 Methyltransferase domain; Region: Methyltransf_11; pfam08241 159087002828 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 159087002829 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087002830 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087002831 metal binding site [ion binding]; metal-binding site 159087002832 active site 159087002833 I-site; other site 159087002834 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 159087002835 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 159087002836 active site 159087002837 DNA binding site [nucleotide binding] 159087002838 Int/Topo IB signature motif; other site 159087002839 Prophage antirepressor [Transcription]; Region: COG3617 159087002840 BRO family, N-terminal domain; Region: Bro-N; smart01040 159087002841 Protein of unknown function (DUF1353); Region: DUF1353; pfam07087 159087002842 KilA-N domain; Region: KilA-N; pfam04383 159087002843 Prophage antirepressor [Transcription]; Region: COG3617 159087002844 BRO family, N-terminal domain; Region: Bro-N; smart01040 159087002845 K-box region; Region: K-box; pfam01486 159087002846 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 159087002847 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 159087002848 catalytic residues [active] 159087002849 catalytic nucleophile [active] 159087002850 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 159087002851 Transcriptional regulator [Transcription]; Region: IclR; COG1414 159087002852 Bacterial transcriptional regulator; Region: IclR; pfam01614 159087002853 ParA-like protein; Provisional; Region: PHA02518 159087002854 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 159087002855 P-loop; other site 159087002856 Magnesium ion binding site [ion binding]; other site 159087002857 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14969 159087002858 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 159087002859 Walker A motif; other site 159087002860 ATP binding site [chemical binding]; other site 159087002861 Walker B motif; other site 159087002862 arginine finger; other site 159087002863 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 159087002864 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 159087002865 hypothetical protein; Validated; Region: PRK00153 159087002866 recombination protein RecR; Reviewed; Region: recR; PRK00076 159087002867 RecR protein; Region: RecR; pfam02132 159087002868 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 159087002869 putative active site [active] 159087002870 putative metal-binding site [ion binding]; other site 159087002871 tetramer interface [polypeptide binding]; other site 159087002872 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 159087002873 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 159087002874 [2Fe-2S] cluster binding site [ion binding]; other site 159087002875 cytochrome b; Provisional; Region: CYTB; MTH00145 159087002876 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 159087002877 Qi binding site; other site 159087002878 intrachain domain interface; other site 159087002879 interchain domain interface [polypeptide binding]; other site 159087002880 heme bH binding site [chemical binding]; other site 159087002881 heme bL binding site [chemical binding]; other site 159087002882 Qo binding site; other site 159087002883 interchain domain interface [polypeptide binding]; other site 159087002884 intrachain domain interface; other site 159087002885 Qi binding site; other site 159087002886 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 159087002887 Qo binding site; other site 159087002888 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 159087002889 stringent starvation protein A; Provisional; Region: sspA; PRK09481 159087002890 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 159087002891 C-terminal domain interface [polypeptide binding]; other site 159087002892 putative GSH binding site (G-site) [chemical binding]; other site 159087002893 dimer interface [polypeptide binding]; other site 159087002894 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 159087002895 dimer interface [polypeptide binding]; other site 159087002896 N-terminal domain interface [polypeptide binding]; other site 159087002897 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 159087002898 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 159087002899 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 159087002900 [4Fe-4S] binding site [ion binding]; other site 159087002901 molybdopterin cofactor binding site; other site 159087002902 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 159087002903 molybdopterin cofactor binding site; other site 159087002904 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 159087002905 glycosyl transferase family protein; Provisional; Region: PRK08136 159087002906 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 159087002907 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 159087002908 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 159087002909 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 159087002910 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 159087002911 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 159087002912 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 159087002913 [2Fe-2S] cluster binding site [ion binding]; other site 159087002914 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 159087002915 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 159087002916 active site 159087002917 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087002918 Catalytic domain of Protein Kinases; Region: PKc; cd00180 159087002919 active site 159087002920 ATP binding site [chemical binding]; other site 159087002921 substrate binding site [chemical binding]; other site 159087002922 activation loop (A-loop); other site 159087002923 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_3; cd04327 159087002924 Astacin (Peptidase family M12A); Region: Astacin; pfam01400 159087002925 active site 159087002926 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 159087002927 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 159087002928 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 159087002929 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087002930 active site 159087002931 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 159087002932 active site 159087002933 ATP binding site [chemical binding]; other site 159087002934 substrate binding site [chemical binding]; other site 159087002935 activation loop (A-loop); other site 159087002936 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 159087002937 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087002938 putative substrate translocation pore; other site 159087002939 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 159087002940 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 159087002941 putative active site [active] 159087002942 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 159087002943 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 159087002944 active site 159087002945 phosphorylation site [posttranslational modification] 159087002946 intermolecular recognition site; other site 159087002947 ANTAR domain; Region: ANTAR; pfam03861 159087002948 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 159087002949 NMT1-like family; Region: NMT1_2; pfam13379 159087002950 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 159087002951 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 159087002952 dimer interface [polypeptide binding]; other site 159087002953 conserved gate region; other site 159087002954 putative PBP binding loops; other site 159087002955 ABC-ATPase subunit interface; other site 159087002956 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 159087002957 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 159087002958 Walker A/P-loop; other site 159087002959 ATP binding site [chemical binding]; other site 159087002960 Q-loop/lid; other site 159087002961 ABC transporter signature motif; other site 159087002962 Walker B; other site 159087002963 D-loop; other site 159087002964 H-loop/switch region; other site 159087002965 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 159087002966 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087002967 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 159087002968 dimerization interface [polypeptide binding]; other site 159087002969 GAF domain; Region: GAF_3; pfam13492 159087002970 Histidine kinase; Region: HisKA_3; pfam07730 159087002971 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 159087002972 ATP binding site [chemical binding]; other site 159087002973 Mg2+ binding site [ion binding]; other site 159087002974 G-X-G motif; other site 159087002975 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087002976 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 159087002977 active site 159087002978 phosphorylation site [posttranslational modification] 159087002979 intermolecular recognition site; other site 159087002980 dimerization interface [polypeptide binding]; other site 159087002981 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 159087002982 DNA binding residues [nucleotide binding] 159087002983 dimerization interface [polypeptide binding]; other site 159087002984 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 159087002985 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 159087002986 dimerization interface [polypeptide binding]; other site 159087002987 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087002988 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087002989 dimer interface [polypeptide binding]; other site 159087002990 putative CheW interface [polypeptide binding]; other site 159087002991 ABC transporter ATPase component; Reviewed; Region: PRK11147 159087002992 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087002993 Walker A/P-loop; other site 159087002994 ATP binding site [chemical binding]; other site 159087002995 Q-loop/lid; other site 159087002996 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087002997 ABC transporter; Region: ABC_tran_2; pfam12848 159087002998 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087002999 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087003000 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 159087003001 putative substrate translocation pore; other site 159087003002 HDOD domain; Region: HDOD; pfam08668 159087003003 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 159087003004 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 159087003005 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 159087003006 endonuclease III; Region: ENDO3c; smart00478 159087003007 minor groove reading motif; other site 159087003008 helix-hairpin-helix signature motif; other site 159087003009 substrate binding pocket [chemical binding]; other site 159087003010 active site 159087003011 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 159087003012 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 159087003013 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 159087003014 Ligand Binding Site [chemical binding]; other site 159087003015 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 159087003016 dihydrodipicolinate synthase; Region: dapA; TIGR00674 159087003017 dimer interface [polypeptide binding]; other site 159087003018 active site 159087003019 catalytic residue [active] 159087003020 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 159087003021 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 159087003022 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 159087003023 TRAM domain; Region: TRAM; cl01282 159087003024 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 159087003025 S-adenosylmethionine binding site [chemical binding]; other site 159087003026 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 159087003027 YccA-like proteins; Region: YccA_like; cd10433 159087003028 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 159087003029 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 159087003030 active site 159087003031 nucleophile elbow; other site 159087003032 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 159087003033 active site 159087003034 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 159087003035 FeS/SAM binding site; other site 159087003036 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 159087003037 non-specific DNA binding site [nucleotide binding]; other site 159087003038 salt bridge; other site 159087003039 sequence-specific DNA binding site [nucleotide binding]; other site 159087003040 FOG: CBS domain [General function prediction only]; Region: COG0517 159087003041 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 159087003042 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 159087003043 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 159087003044 Tetramer interface [polypeptide binding]; other site 159087003045 active site 159087003046 FMN-binding site [chemical binding]; other site 159087003047 Protein of unknown function (DUF465); Region: DUF465; cl01070 159087003048 MFS_1 like family; Region: MFS_1_like; pfam12832 159087003049 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 159087003050 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 159087003051 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 159087003052 substrate binding site [chemical binding]; other site 159087003053 ligand binding site [chemical binding]; other site 159087003054 Entericidin EcnA/B family; Region: Entericidin; cl02322 159087003055 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 159087003056 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 159087003057 substrate binding site [chemical binding]; other site 159087003058 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 159087003059 tartrate dehydrogenase; Region: TTC; TIGR02089 159087003060 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 159087003061 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 159087003062 FimV N-terminal domain; Region: FimV_core; TIGR03505 159087003063 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 159087003064 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 159087003065 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 159087003066 dimerization interface 3.5A [polypeptide binding]; other site 159087003067 active site 159087003068 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 159087003069 active site 159087003070 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 159087003071 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 159087003072 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087003073 catalytic residue [active] 159087003074 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 159087003075 substrate binding site [chemical binding]; other site 159087003076 active site 159087003077 catalytic residues [active] 159087003078 heterodimer interface [polypeptide binding]; other site 159087003079 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 159087003080 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 159087003081 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 159087003082 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 159087003083 Sporulation related domain; Region: SPOR; pfam05036 159087003084 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 159087003085 Colicin V production protein; Region: Colicin_V; pfam02674 159087003086 amidophosphoribosyltransferase; Provisional; Region: PRK09246 159087003087 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 159087003088 tetramer interface [polypeptide binding]; other site 159087003089 active site 159087003090 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 159087003091 active site 159087003092 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 159087003093 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 159087003094 homodimer interface [polypeptide binding]; other site 159087003095 substrate-cofactor binding pocket; other site 159087003096 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087003097 catalytic residue [active] 159087003098 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 159087003099 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 159087003100 ATP binding site [chemical binding]; other site 159087003101 Mg++ binding site [ion binding]; other site 159087003102 motif III; other site 159087003103 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 159087003104 nucleotide binding region [chemical binding]; other site 159087003105 ATP-binding site [chemical binding]; other site 159087003106 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 159087003107 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 159087003108 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 159087003109 Walker A motif; other site 159087003110 ATP binding site [chemical binding]; other site 159087003111 Walker B motif; other site 159087003112 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 159087003113 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 159087003114 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 159087003115 legume lectins; Region: lectin_L-type; cl14058 159087003116 homotetramer interaction site [polypeptide binding]; other site 159087003117 homodimer interaction site [polypeptide binding]; other site 159087003118 carbohydrate binding site [chemical binding]; other site 159087003119 metal binding site [ion binding]; metal-binding site 159087003120 Secretin and TonB N terminus short domain; Region: STN; smart00965 159087003121 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 159087003122 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 159087003123 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087003124 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 159087003125 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 159087003126 Walker A motif; other site 159087003127 ATP binding site [chemical binding]; other site 159087003128 Walker B motif; other site 159087003129 arginine finger; other site 159087003130 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 159087003131 binding surface 159087003132 TPR motif; other site 159087003133 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 159087003134 TPR motif; other site 159087003135 binding surface 159087003136 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 159087003137 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087003138 acyl-activating enzyme (AAE) consensus motif; other site 159087003139 AMP binding site [chemical binding]; other site 159087003140 active site 159087003141 CoA binding site [chemical binding]; other site 159087003142 DNA-binding transcriptional activator MhpR; Provisional; Region: PRK09834 159087003143 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 159087003144 Bacterial transcriptional regulator; Region: IclR; pfam01614 159087003145 Transcriptional regulators [Transcription]; Region: GntR; COG1802 159087003146 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087003147 DNA-binding site [nucleotide binding]; DNA binding site 159087003148 FCD domain; Region: FCD; pfam07729 159087003149 FAD binding domain; Region: FAD_binding_3; pfam01494 159087003150 hypothetical protein; Provisional; Region: PRK07236 159087003151 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087003152 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087003153 putative ligand binding site [chemical binding]; other site 159087003154 Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), which catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate; Region: MhpB_like; cd07365 159087003155 putative active site [active] 159087003156 Fe(II) binding site [ion binding]; other site 159087003157 putative dimer interface [polypeptide binding]; other site 159087003158 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 159087003159 putative tetramer interface [polypeptide binding]; other site 159087003160 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 159087003161 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087003162 active site 159087003163 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 159087003164 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087003165 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087003166 putative ligand binding site [chemical binding]; other site 159087003167 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087003168 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087003169 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 159087003170 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087003171 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087003172 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087003173 active site 159087003174 catalytic residues [active] 159087003175 metal binding site [ion binding]; metal-binding site 159087003176 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087003177 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087003178 TM-ABC transporter signature motif; other site 159087003179 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087003180 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087003181 TM-ABC transporter signature motif; other site 159087003182 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087003183 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087003184 Walker A/P-loop; other site 159087003185 ATP binding site [chemical binding]; other site 159087003186 Q-loop/lid; other site 159087003187 ABC transporter signature motif; other site 159087003188 Walker B; other site 159087003189 D-loop; other site 159087003190 H-loop/switch region; other site 159087003191 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087003192 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087003193 Walker A/P-loop; other site 159087003194 ATP binding site [chemical binding]; other site 159087003195 Q-loop/lid; other site 159087003196 ABC transporter signature motif; other site 159087003197 Walker B; other site 159087003198 D-loop; other site 159087003199 H-loop/switch region; other site 159087003200 Hemerythrin-like domain; Region: Hr-like; cd12108 159087003201 Fe binding site [ion binding]; other site 159087003202 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087003203 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 159087003204 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 159087003205 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 159087003206 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 159087003207 ATP binding site [chemical binding]; other site 159087003208 putative Mg++ binding site [ion binding]; other site 159087003209 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 159087003210 nucleotide binding region [chemical binding]; other site 159087003211 ATP-binding site [chemical binding]; other site 159087003212 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 159087003213 HRDC domain; Region: HRDC; pfam00570 159087003214 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 159087003215 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 159087003216 putative active site [active] 159087003217 putative metal binding site [ion binding]; other site 159087003218 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 159087003219 substrate binding site [chemical binding]; other site 159087003220 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 159087003221 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 159087003222 substrate binding site [chemical binding]; other site 159087003223 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 159087003224 SnoaL-like domain; Region: SnoaL_3; pfam13474 159087003225 TPR repeat; Region: TPR_11; pfam13414 159087003226 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 159087003227 binding surface 159087003228 TPR motif; other site 159087003229 Tetratricopeptide repeat; Region: TPR_16; pfam13432 159087003230 SnoaL-like domain; Region: SnoaL_3; pfam13474 159087003231 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 159087003232 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 159087003233 active site 159087003234 HIGH motif; other site 159087003235 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 159087003236 KMSKS motif; other site 159087003237 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 159087003238 tRNA binding surface [nucleotide binding]; other site 159087003239 anticodon binding site; other site 159087003240 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087003241 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087003242 putative ligand binding site [chemical binding]; other site 159087003243 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087003244 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087003245 putative ligand binding site [chemical binding]; other site 159087003246 chaperone protein DnaJ; Provisional; Region: PRK10767 159087003247 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 159087003248 HSP70 interaction site [polypeptide binding]; other site 159087003249 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 159087003250 substrate binding site [polypeptide binding]; other site 159087003251 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 159087003252 Zn binding sites [ion binding]; other site 159087003253 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 159087003254 dimer interface [polypeptide binding]; other site 159087003255 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 159087003256 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 159087003257 nucleotide binding site [chemical binding]; other site 159087003258 GrpE; Region: GrpE; pfam01025 159087003259 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 159087003260 dimer interface [polypeptide binding]; other site 159087003261 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 159087003262 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 159087003263 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087003264 active site 159087003265 ATP binding site [chemical binding]; other site 159087003266 substrate binding site [chemical binding]; other site 159087003267 activation loop (A-loop); other site 159087003268 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 159087003269 ligand binding site [chemical binding]; other site 159087003270 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 159087003271 dimerization interface [polypeptide binding]; other site 159087003272 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087003273 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087003274 dimer interface [polypeptide binding]; other site 159087003275 putative CheW interface [polypeptide binding]; other site 159087003276 thioredoxin 2; Provisional; Region: PRK10996 159087003277 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 159087003278 catalytic residues [active] 159087003279 ferrochelatase; Reviewed; Region: hemH; PRK00035 159087003280 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 159087003281 C-terminal domain interface [polypeptide binding]; other site 159087003282 active site 159087003283 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 159087003284 active site 159087003285 N-terminal domain interface [polypeptide binding]; other site 159087003286 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 159087003287 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 159087003288 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 159087003289 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 159087003290 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 159087003291 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 159087003292 Walker A/P-loop; other site 159087003293 ATP binding site [chemical binding]; other site 159087003294 Q-loop/lid; other site 159087003295 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 159087003296 ABC transporter signature motif; other site 159087003297 Walker B; other site 159087003298 D-loop; other site 159087003299 H-loop/switch region; other site 159087003300 Predicted membrane protein [Function unknown]; Region: COG2119 159087003301 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 159087003302 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 159087003303 ferric uptake regulator; Provisional; Region: fur; PRK09462 159087003304 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 159087003305 metal binding site 2 [ion binding]; metal-binding site 159087003306 putative DNA binding helix; other site 159087003307 metal binding site 1 [ion binding]; metal-binding site 159087003308 dimer interface [polypeptide binding]; other site 159087003309 structural Zn2+ binding site [ion binding]; other site 159087003310 outer membrane biogenesis protein BamE; Provisional; Region: PRK11548 159087003311 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 159087003312 dihydrodipicolinate reductase; Provisional; Region: PRK00048 159087003313 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 159087003314 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 159087003315 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 159087003316 putative active site [active] 159087003317 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087003318 heme pocket [chemical binding]; other site 159087003319 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 159087003320 dimer interface [polypeptide binding]; other site 159087003321 phosphorylation site [posttranslational modification] 159087003322 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 159087003323 ATP binding site [chemical binding]; other site 159087003324 Mg2+ binding site [ion binding]; other site 159087003325 G-X-G motif; other site 159087003326 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087003327 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003328 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 159087003329 active site 159087003330 phosphorylation site [posttranslational modification] 159087003331 intermolecular recognition site; other site 159087003332 dimerization interface [polypeptide binding]; other site 159087003333 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 159087003334 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 159087003335 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 159087003336 catalytic site [active] 159087003337 subunit interface [polypeptide binding]; other site 159087003338 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 159087003339 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087003340 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 159087003341 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 159087003342 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087003343 ATP-grasp domain; Region: ATP-grasp_4; cl17255 159087003344 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 159087003345 IMP binding site; other site 159087003346 dimer interface [polypeptide binding]; other site 159087003347 interdomain contacts; other site 159087003348 partial ornithine binding site; other site 159087003349 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 159087003350 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 159087003351 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 159087003352 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 159087003353 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 159087003354 FtsJ-like methyltransferase; Region: FtsJ; cl17430 159087003355 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 159087003356 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 159087003357 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 159087003358 Walker A motif; other site 159087003359 ATP binding site [chemical binding]; other site 159087003360 Walker B motif; other site 159087003361 arginine finger; other site 159087003362 Peptidase family M41; Region: Peptidase_M41; pfam01434 159087003363 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 159087003364 dihydropteroate synthase; Region: DHPS; TIGR01496 159087003365 substrate binding pocket [chemical binding]; other site 159087003366 dimer interface [polypeptide binding]; other site 159087003367 inhibitor binding site; inhibition site 159087003368 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 159087003369 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 159087003370 active site 159087003371 substrate binding site [chemical binding]; other site 159087003372 metal binding site [ion binding]; metal-binding site 159087003373 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 159087003374 substrate binding site [chemical binding]; other site 159087003375 dimer interface [polypeptide binding]; other site 159087003376 catalytic triad [active] 159087003377 Preprotein translocase SecG subunit; Region: SecG; pfam03840 159087003378 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 159087003379 NADH dehydrogenase subunit B; Validated; Region: PRK06411 159087003380 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 159087003381 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 159087003382 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 159087003383 NADH dehydrogenase subunit D; Validated; Region: PRK06075 159087003384 NADH dehydrogenase subunit E; Validated; Region: PRK07539 159087003385 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 159087003386 putative dimer interface [polypeptide binding]; other site 159087003387 [2Fe-2S] cluster binding site [ion binding]; other site 159087003388 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 159087003389 SLBB domain; Region: SLBB; pfam10531 159087003390 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 159087003391 NADH dehydrogenase subunit G; Validated; Region: PRK09129 159087003392 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 159087003393 catalytic loop [active] 159087003394 iron binding site [ion binding]; other site 159087003395 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 159087003396 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 159087003397 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 159087003398 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 159087003399 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 159087003400 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 159087003401 4Fe-4S binding domain; Region: Fer4; cl02805 159087003402 4Fe-4S binding domain; Region: Fer4; pfam00037 159087003403 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 159087003404 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 159087003405 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 159087003406 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 159087003407 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 159087003408 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 159087003409 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 159087003410 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 159087003411 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 159087003412 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 159087003413 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 159087003414 GDP-mannose pyrophosphatase NudK; Provisional; Region: PRK15009 159087003415 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 159087003416 dimer interface [polypeptide binding]; other site 159087003417 ADP-ribose binding site [chemical binding]; other site 159087003418 active site 159087003419 nudix motif; other site 159087003420 metal binding site [ion binding]; metal-binding site 159087003421 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 159087003422 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 159087003423 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 159087003424 active site 159087003425 dimer interface [polypeptide binding]; other site 159087003426 effector binding site; other site 159087003427 Hemerythrin; Region: Hemerythrin; cd12107 159087003428 Fe binding site [ion binding]; other site 159087003429 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 159087003430 PAS domain; Region: PAS_9; pfam13426 159087003431 putative active site [active] 159087003432 heme pocket [chemical binding]; other site 159087003433 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 159087003434 dimer interface [polypeptide binding]; other site 159087003435 phosphorylation site [posttranslational modification] 159087003436 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 159087003437 ATP binding site [chemical binding]; other site 159087003438 Mg2+ binding site [ion binding]; other site 159087003439 G-X-G motif; other site 159087003440 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003441 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 159087003442 active site 159087003443 phosphorylation site [posttranslational modification] 159087003444 intermolecular recognition site; other site 159087003445 dimerization interface [polypeptide binding]; other site 159087003446 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 159087003447 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 159087003448 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 159087003449 Walker A motif; other site 159087003450 ATP binding site [chemical binding]; other site 159087003451 Walker B motif; other site 159087003452 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087003453 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 159087003454 dimer interface [polypeptide binding]; other site 159087003455 phosphorylation site [posttranslational modification] 159087003456 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 159087003457 ATP binding site [chemical binding]; other site 159087003458 Mg2+ binding site [ion binding]; other site 159087003459 G-X-G motif; other site 159087003460 GTPase SAR1 and related small G proteins [General function prediction only]; Region: COG1100 159087003461 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 159087003462 G1 box; other site 159087003463 GTP/Mg2+ binding site [chemical binding]; other site 159087003464 G2 box; other site 159087003465 Switch I region; other site 159087003466 G3 box; other site 159087003467 Switch II region; other site 159087003468 G4 box; other site 159087003469 G5 box; other site 159087003470 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003471 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 159087003472 active site 159087003473 phosphorylation site [posttranslational modification] 159087003474 intermolecular recognition site; other site 159087003475 dimerization interface [polypeptide binding]; other site 159087003476 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087003477 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 159087003478 active site 159087003479 phosphorylation site [posttranslational modification] 159087003480 intermolecular recognition site; other site 159087003481 dimerization interface [polypeptide binding]; other site 159087003482 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087003483 Zn2+ binding site [ion binding]; other site 159087003484 Mg2+ binding site [ion binding]; other site 159087003485 PAS domain S-box; Region: sensory_box; TIGR00229 159087003486 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 159087003487 putative active site [active] 159087003488 heme pocket [chemical binding]; other site 159087003489 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 159087003490 PAS fold; Region: PAS_3; pfam08447 159087003491 putative active site [active] 159087003492 heme pocket [chemical binding]; other site 159087003493 GAF domain; Region: GAF_2; pfam13185 159087003494 GAF domain; Region: GAF; pfam01590 159087003495 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 159087003496 PAS fold; Region: PAS_3; pfam08447 159087003497 putative active site [active] 159087003498 heme pocket [chemical binding]; other site 159087003499 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087003500 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 159087003501 dimer interface [polypeptide binding]; other site 159087003502 phosphorylation site [posttranslational modification] 159087003503 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 159087003504 ATP binding site [chemical binding]; other site 159087003505 Mg2+ binding site [ion binding]; other site 159087003506 G-X-G motif; other site 159087003507 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087003508 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 159087003509 active site 159087003510 phosphorylation site [posttranslational modification] 159087003511 intermolecular recognition site; other site 159087003512 dimerization interface [polypeptide binding]; other site 159087003513 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 159087003514 PAS fold; Region: PAS_3; pfam08447 159087003515 putative active site [active] 159087003516 heme pocket [chemical binding]; other site 159087003517 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 159087003518 PAS domain; Region: PAS_9; pfam13426 159087003519 putative active site [active] 159087003520 heme pocket [chemical binding]; other site 159087003521 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087003522 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087003523 metal binding site [ion binding]; metal-binding site 159087003524 active site 159087003525 I-site; other site 159087003526 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 159087003527 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003528 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 159087003529 active site 159087003530 phosphorylation site [posttranslational modification] 159087003531 intermolecular recognition site; other site 159087003532 dimerization interface [polypeptide binding]; other site 159087003533 PAS fold; Region: PAS_4; pfam08448 159087003534 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087003535 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 159087003536 putative active site [active] 159087003537 heme pocket [chemical binding]; other site 159087003538 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 159087003539 dimer interface [polypeptide binding]; other site 159087003540 phosphorylation site [posttranslational modification] 159087003541 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 159087003542 ATP binding site [chemical binding]; other site 159087003543 Mg2+ binding site [ion binding]; other site 159087003544 G-X-G motif; other site 159087003545 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003546 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 159087003547 active site 159087003548 phosphorylation site [posttranslational modification] 159087003549 intermolecular recognition site; other site 159087003550 dimerization interface [polypeptide binding]; other site 159087003551 Acetokinase family; Region: Acetate_kinase; cl17229 159087003552 propionate/acetate kinase; Provisional; Region: PRK12379 159087003553 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 159087003554 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 159087003555 dimer interaction site [polypeptide binding]; other site 159087003556 substrate-binding tunnel; other site 159087003557 active site 159087003558 catalytic site [active] 159087003559 substrate binding site [chemical binding]; other site 159087003560 phosphate acetyltransferase; Provisional; Region: PRK11890 159087003561 Predicted protein tyrosine phosphatase [General function prediction only]; Region: COG5350 159087003562 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK07533 159087003563 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 159087003564 NAD binding site [chemical binding]; other site 159087003565 homotetramer interface [polypeptide binding]; other site 159087003566 homodimer interface [polypeptide binding]; other site 159087003567 substrate binding site [chemical binding]; other site 159087003568 active site 159087003569 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 159087003570 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase...; Region: TRX_Fd_NuoE_hoxF; cd03083 159087003571 putative dimer interface [polypeptide binding]; other site 159087003572 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 159087003573 SLBB domain; Region: SLBB; pfam10531 159087003574 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 159087003575 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 159087003576 catalytic loop [active] 159087003577 iron binding site [ion binding]; other site 159087003578 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 159087003579 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 159087003580 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 159087003581 Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit...; Region: H2MP_NAD-link-bidir; cd06066 159087003582 nickel binding site [ion binding]; other site 159087003583 phosphoserine aminotransferase; Provisional; Region: PRK12462 159087003584 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087003585 catalytic residue [active] 159087003586 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 159087003587 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 159087003588 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087003589 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 159087003590 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 159087003591 Walker A/P-loop; other site 159087003592 ATP binding site [chemical binding]; other site 159087003593 Q-loop/lid; other site 159087003594 ABC transporter signature motif; other site 159087003595 Walker B; other site 159087003596 D-loop; other site 159087003597 H-loop/switch region; other site 159087003598 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 159087003599 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 159087003600 Walker A/P-loop; other site 159087003601 ATP binding site [chemical binding]; other site 159087003602 Q-loop/lid; other site 159087003603 ABC transporter signature motif; other site 159087003604 Walker B; other site 159087003605 D-loop; other site 159087003606 H-loop/switch region; other site 159087003607 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 159087003608 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 159087003609 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 159087003610 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 159087003611 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 159087003612 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 159087003613 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 159087003614 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 159087003615 Ligand Binding Site [chemical binding]; other site 159087003616 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 159087003617 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087003618 Beta-Casp domain; Region: Beta-Casp; smart01027 159087003619 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 159087003620 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 159087003621 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 159087003622 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087003623 putative CheW interface [polypeptide binding]; other site 159087003624 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 159087003625 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 159087003626 Hemerythrin-like domain; Region: Hr-like; cd12108 159087003627 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 159087003628 CPxP motif; other site 159087003629 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 159087003630 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 159087003631 GAF domain; Region: GAF; pfam01590 159087003632 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 159087003633 Walker A motif; other site 159087003634 ATP binding site [chemical binding]; other site 159087003635 Walker B motif; other site 159087003636 arginine finger; other site 159087003637 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 159087003638 DNA-binding interface [nucleotide binding]; DNA binding site 159087003639 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 159087003640 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 159087003641 membrane-bound complex binding site; other site 159087003642 hinge residues; other site 159087003643 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 159087003644 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 159087003645 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 159087003646 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 159087003647 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 159087003648 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 159087003649 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 159087003650 dimer interface [polypeptide binding]; other site 159087003651 phosphorylation site [posttranslational modification] 159087003652 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 159087003653 ATP binding site [chemical binding]; other site 159087003654 Mg2+ binding site [ion binding]; other site 159087003655 G-X-G motif; other site 159087003656 Cytochrome c; Region: Cytochrom_C; cl11414 159087003657 Protein of unknown function (DUF779); Region: DUF779; pfam05610 159087003658 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 159087003659 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 159087003660 NAD(P) binding site [chemical binding]; other site 159087003661 catalytic residues [active] 159087003662 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087003663 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 159087003664 dimer interface [polypeptide binding]; other site 159087003665 phosphorylation site [posttranslational modification] 159087003666 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 159087003667 ATP binding site [chemical binding]; other site 159087003668 Mg2+ binding site [ion binding]; other site 159087003669 G-X-G motif; other site 159087003670 Response regulator receiver domain; Region: Response_reg; pfam00072 159087003671 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 159087003672 active site 159087003673 phosphorylation site [posttranslational modification] 159087003674 intermolecular recognition site; other site 159087003675 dimerization interface [polypeptide binding]; other site 159087003676 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 159087003677 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 159087003678 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 159087003679 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 159087003680 Immunoglobulin I-set domain; Region: I-set; pfam07679 159087003681 Immunoglobulin like; Region: IG_like; smart00410 159087003682 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 159087003683 active site 159087003684 catalytic site [active] 159087003685 substrate binding site [chemical binding]; other site 159087003686 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 159087003687 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087003688 putative substrate translocation pore; other site 159087003689 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 159087003690 Transglycosylase; Region: Transgly; pfam00912 159087003691 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 159087003692 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 159087003693 GAF domain; Region: GAF; pfam01590 159087003694 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 159087003695 Walker A motif; other site 159087003696 ATP binding site [chemical binding]; other site 159087003697 Walker B motif; other site 159087003698 arginine finger; other site 159087003699 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087003700 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 159087003701 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 159087003702 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 159087003703 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 159087003704 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 159087003705 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 159087003706 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 159087003707 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 159087003708 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 159087003709 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 159087003710 Cytochrome c; Region: Cytochrom_C; cl11414 159087003711 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 159087003712 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 159087003713 dimer interface [polypeptide binding]; other site 159087003714 Trp docking motif [polypeptide binding]; other site 159087003715 active site 159087003716 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 159087003717 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 159087003718 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087003719 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; cl17818 159087003720 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 159087003721 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087003722 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 159087003723 N-terminal plug; other site 159087003724 ligand-binding site [chemical binding]; other site 159087003725 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 159087003726 dimerization interface [polypeptide binding]; other site 159087003727 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 159087003728 Histidine kinase; Region: HisKA_3; pfam07730 159087003729 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 159087003730 ATP binding site [chemical binding]; other site 159087003731 Mg2+ binding site [ion binding]; other site 159087003732 G-X-G motif; other site 159087003733 response regulator; Provisional; Region: PRK09483 159087003734 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 159087003735 active site 159087003736 phosphorylation site [posttranslational modification] 159087003737 intermolecular recognition site; other site 159087003738 dimerization interface [polypeptide binding]; other site 159087003739 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 159087003740 DNA binding residues [nucleotide binding] 159087003741 dimerization interface [polypeptide binding]; other site 159087003742 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 159087003743 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 159087003744 PLD-like domain; Region: PLDc_2; pfam13091 159087003745 homodimer interface [polypeptide binding]; other site 159087003746 putative active site [active] 159087003747 catalytic site [active] 159087003748 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 159087003749 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 159087003750 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 159087003751 catalytic residues [active] 159087003752 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087003753 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 159087003754 ligand binding site [chemical binding]; other site 159087003755 flexible hinge region; other site 159087003756 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 159087003757 integrase; Provisional; Region: int; PHA02601 159087003758 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 159087003759 active site 159087003760 DNA binding site [nucleotide binding] 159087003761 Int/Topo IB signature motif; other site 159087003762 Helix-turn-helix domain; Region: HTH_17; pfam12728 159087003763 Protein of unknown function (DUF3087); Region: DUF3087; pfam11286 159087003764 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 159087003765 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 159087003766 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087003767 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 159087003768 N-terminal plug; other site 159087003769 ligand-binding site [chemical binding]; other site 159087003770 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 159087003771 Domain of unknown function DUF302; Region: DUF302; cl01364 159087003772 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 159087003773 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 159087003774 ligand binding site [chemical binding]; other site 159087003775 flexible hinge region; other site 159087003776 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 159087003777 putative switch regulator; other site 159087003778 non-specific DNA interactions [nucleotide binding]; other site 159087003779 DNA binding site [nucleotide binding] 159087003780 sequence specific DNA binding site [nucleotide binding]; other site 159087003781 putative cAMP binding site [chemical binding]; other site 159087003782 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 159087003783 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 159087003784 FeS/SAM binding site; other site 159087003785 HemN C-terminal domain; Region: HemN_C; pfam06969 159087003786 Family description; Region: DsbD_2; pfam13386 159087003787 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 159087003788 Ligand Binding Site [chemical binding]; other site 159087003789 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087003790 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 159087003791 metal-binding site [ion binding] 159087003792 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087003793 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 159087003794 motif II; other site 159087003795 PAS domain S-box; Region: sensory_box; TIGR00229 159087003796 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 159087003797 putative active site [active] 159087003798 heme pocket [chemical binding]; other site 159087003799 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087003800 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087003801 metal binding site [ion binding]; metal-binding site 159087003802 active site 159087003803 I-site; other site 159087003804 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 159087003805 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 159087003806 metal-binding site [ion binding] 159087003807 selenophosphate synthetase; Provisional; Region: PRK00943 159087003808 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 159087003809 dimerization interface [polypeptide binding]; other site 159087003810 putative ATP binding site [chemical binding]; other site 159087003811 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 159087003812 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 159087003813 N-terminal plug; other site 159087003814 ligand-binding site [chemical binding]; other site 159087003815 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 159087003816 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 159087003817 Protein of unknown function (DUF1513); Region: DUF1513; pfam07433 159087003818 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 159087003819 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 159087003820 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 159087003821 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 159087003822 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 159087003823 heme binding site [chemical binding]; other site 159087003824 ferroxidase pore; other site 159087003825 ferroxidase diiron center [ion binding]; other site 159087003826 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 159087003827 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 159087003828 heme binding site [chemical binding]; other site 159087003829 ferroxidase pore; other site 159087003830 ferroxidase diiron center [ion binding]; other site 159087003831 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 159087003832 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087003833 DNA-binding site [nucleotide binding]; DNA binding site 159087003834 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 159087003835 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087003836 homodimer interface [polypeptide binding]; other site 159087003837 catalytic residue [active] 159087003838 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 159087003839 Subunit I/III interface [polypeptide binding]; other site 159087003840 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087003841 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087003842 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 159087003843 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 159087003844 FeoA domain; Region: FeoA; pfam04023 159087003845 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 159087003846 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 159087003847 G1 box; other site 159087003848 GTP/Mg2+ binding site [chemical binding]; other site 159087003849 Switch I region; other site 159087003850 G2 box; other site 159087003851 G3 box; other site 159087003852 Switch II region; other site 159087003853 G4 box; other site 159087003854 G5 box; other site 159087003855 Nucleoside recognition; Region: Gate; pfam07670 159087003856 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 159087003857 Nucleoside recognition; Region: Gate; pfam07670 159087003858 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 159087003859 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 159087003860 conserved cys residue [active] 159087003861 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087003862 CheW-like domain; Region: CheW; pfam01584 159087003863 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 159087003864 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087003865 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 159087003866 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 159087003867 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 159087003868 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 159087003869 putative NADH binding site [chemical binding]; other site 159087003870 putative active site [active] 159087003871 nudix motif; other site 159087003872 putative metal binding site [ion binding]; other site 159087003873 Membrane protein of unknown function; Region: DUF360; pfam04020 159087003874 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 159087003875 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 159087003876 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 159087003877 putative substrate translocation pore; other site 159087003878 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 159087003879 CoenzymeA binding site [chemical binding]; other site 159087003880 subunit interaction site [polypeptide binding]; other site 159087003881 PHB binding site; other site 159087003882 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 159087003883 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 159087003884 active site 159087003885 phosphorylation site [posttranslational modification] 159087003886 intermolecular recognition site; other site 159087003887 dimerization interface [polypeptide binding]; other site 159087003888 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 159087003889 DNA binding site [nucleotide binding] 159087003890 sensor protein KdpD; Provisional; Region: PRK10490 159087003891 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 159087003892 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 159087003893 Ligand Binding Site [chemical binding]; other site 159087003894 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 159087003895 GAF domain; Region: GAF_3; pfam13492 159087003896 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 159087003897 dimer interface [polypeptide binding]; other site 159087003898 phosphorylation site [posttranslational modification] 159087003899 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 159087003900 ATP binding site [chemical binding]; other site 159087003901 Mg2+ binding site [ion binding]; other site 159087003902 G-X-G motif; other site 159087003903 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 159087003904 Mycobacterium tuberculosis CorA-like subfamily; Region: MtCorA-like; cd12830 159087003905 oligomer interface [polypeptide binding]; other site 159087003906 metal binding site [ion binding]; metal-binding site 159087003907 metal binding site [ion binding]; metal-binding site 159087003908 putative Cl binding site [ion binding]; other site 159087003909 basic sphincter; other site 159087003910 hydrophobic gate; other site 159087003911 periplasmic entrance; other site 159087003912 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 159087003913 active site 159087003914 phosphorylation site [posttranslational modification] 159087003915 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 159087003916 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 159087003917 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 159087003918 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087003919 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 159087003920 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 159087003921 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087003922 ligand binding site [chemical binding]; other site 159087003923 flexible hinge region; other site 159087003924 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 159087003925 putative switch regulator; other site 159087003926 non-specific DNA interactions [nucleotide binding]; other site 159087003927 DNA binding site [nucleotide binding] 159087003928 sequence specific DNA binding site [nucleotide binding]; other site 159087003929 putative cAMP binding site [chemical binding]; other site 159087003930 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 159087003931 catalytic residues [active] 159087003932 dimer interface [polypeptide binding]; other site 159087003933 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 159087003934 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 159087003935 active site 2 [active] 159087003936 active site 1 [active] 159087003937 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 159087003938 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087003939 Zn2+ binding site [ion binding]; other site 159087003940 Mg2+ binding site [ion binding]; other site 159087003941 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 159087003942 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 159087003943 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 159087003944 putative substrate translocation pore; other site 159087003945 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 159087003946 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 159087003947 EamA-like transporter family; Region: EamA; pfam00892 159087003948 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 159087003949 EamA-like transporter family; Region: EamA; pfam00892 159087003950 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 159087003951 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 159087003952 FMN binding site [chemical binding]; other site 159087003953 active site 159087003954 substrate binding site [chemical binding]; other site 159087003955 catalytic residue [active] 159087003956 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087003957 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087003958 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 159087003959 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087003960 Zn2+ binding site [ion binding]; other site 159087003961 Mg2+ binding site [ion binding]; other site 159087003962 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 159087003963 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 159087003964 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087003965 AAA domain; Region: AAA_21; pfam13304 159087003966 Walker A/P-loop; other site 159087003967 ATP binding site [chemical binding]; other site 159087003968 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087003969 Walker B; other site 159087003970 D-loop; other site 159087003971 H-loop/switch region; other site 159087003972 Nuclease-related domain; Region: NERD; pfam08378 159087003973 Part of AAA domain; Region: AAA_19; pfam13245 159087003974 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 159087003975 Family description; Region: UvrD_C_2; pfam13538 159087003976 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 159087003977 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087003978 Iron permease FTR1 family; Region: FTR1; cl00475 159087003979 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 159087003980 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 159087003981 Fe2+ transport protein; Region: Iron_transport; pfam10634 159087003982 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 159087003983 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 159087003984 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 159087003985 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 159087003986 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 159087003987 Hemin uptake protein hemP; Region: hemP; pfam10636 159087003988 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 159087003989 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087003990 ATP binding site [chemical binding]; other site 159087003991 Mg++ binding site [ion binding]; other site 159087003992 motif III; other site 159087003993 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 159087003994 nucleotide binding region [chemical binding]; other site 159087003995 ATP-binding site [chemical binding]; other site 159087003996 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 159087003997 putative RNA binding site [nucleotide binding]; other site 159087003998 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 159087003999 dinuclear metal binding motif [ion binding]; other site 159087004000 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 159087004001 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 159087004002 active site 159087004003 catalytic tetrad [active] 159087004004 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 159087004005 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 159087004006 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 159087004007 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 159087004008 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 159087004009 heat shock protein 90; Provisional; Region: PRK05218 159087004010 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 159087004011 ATP binding site [chemical binding]; other site 159087004012 Mg2+ binding site [ion binding]; other site 159087004013 G-X-G motif; other site 159087004014 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 159087004015 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 159087004016 ATP binding site [chemical binding]; other site 159087004017 Mg++ binding site [ion binding]; other site 159087004018 motif III; other site 159087004019 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 159087004020 nucleotide binding region [chemical binding]; other site 159087004021 ATP-binding site [chemical binding]; other site 159087004022 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 159087004023 putative RNA binding site [nucleotide binding]; other site 159087004024 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 159087004025 ABC1 family; Region: ABC1; pfam03109 159087004026 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 159087004027 MucB/RseB family; Region: MucB_RseB; pfam03888 159087004028 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 159087004029 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 159087004030 putative substrate translocation pore; other site 159087004031 transcriptional activator TtdR; Provisional; Region: PRK09801 159087004032 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087004033 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 159087004034 putative effector binding pocket; other site 159087004035 putative dimerization interface [polypeptide binding]; other site 159087004036 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087004037 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 159087004038 Response regulator receiver domain; Region: Response_reg; pfam00072 159087004039 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 159087004040 active site 159087004041 phosphorylation site [posttranslational modification] 159087004042 intermolecular recognition site; other site 159087004043 dimerization interface [polypeptide binding]; other site 159087004044 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087004045 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 159087004046 anti sigma factor interaction site; other site 159087004047 regulatory phosphorylation site [posttranslational modification]; other site 159087004048 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 159087004049 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 159087004050 putative binding surface; other site 159087004051 active site 159087004052 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 159087004053 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 159087004054 ATP binding site [chemical binding]; other site 159087004055 Mg2+ binding site [ion binding]; other site 159087004056 G-X-G motif; other site 159087004057 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 159087004058 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 159087004059 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 159087004060 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 159087004061 dimerization interface [polypeptide binding]; other site 159087004062 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087004063 dimer interface [polypeptide binding]; other site 159087004064 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 159087004065 putative CheW interface [polypeptide binding]; other site 159087004066 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 159087004067 CheD chemotactic sensory transduction; Region: CheD; cl00810 159087004068 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 159087004069 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 159087004070 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 159087004071 CheD chemotactic sensory transduction; Region: CheD; cl00810 159087004072 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 159087004073 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 159087004074 active site 159087004075 phosphorylation site [posttranslational modification] 159087004076 intermolecular recognition site; other site 159087004077 dimerization interface [polypeptide binding]; other site 159087004078 CheB methylesterase; Region: CheB_methylest; pfam01339 159087004079 HDOD domain; Region: HDOD; pfam08668 159087004080 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; smart00471 159087004081 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 159087004082 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 159087004083 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 159087004084 Walker A motif; other site 159087004085 ATP binding site [chemical binding]; other site 159087004086 Walker B motif; other site 159087004087 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 159087004088 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087004089 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 159087004090 FIST C domain; Region: FIST_C; pfam10442 159087004091 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 159087004092 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 159087004093 minor groove reading motif; other site 159087004094 helix-hairpin-helix signature motif; other site 159087004095 substrate binding pocket [chemical binding]; other site 159087004096 active site 159087004097 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 159087004098 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 159087004099 PAS domain; Region: PAS_9; pfam13426 159087004100 putative active site [active] 159087004101 heme pocket [chemical binding]; other site 159087004102 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 159087004103 PAS domain; Region: PAS_9; pfam13426 159087004104 putative active site [active] 159087004105 heme pocket [chemical binding]; other site 159087004106 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087004107 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087004108 metal binding site [ion binding]; metal-binding site 159087004109 active site 159087004110 I-site; other site 159087004111 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14464 159087004112 electron transport complex RsxE subunit; Provisional; Region: PRK12405 159087004113 FMN-binding domain; Region: FMN_bind; cl01081 159087004114 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 159087004115 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 159087004116 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 159087004117 SLBB domain; Region: SLBB; pfam10531 159087004118 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 159087004119 electron transport complex protein RnfB; Provisional; Region: PRK05113 159087004120 Putative Fe-S cluster; Region: FeS; pfam04060 159087004121 4Fe-4S binding domain; Region: Fer4; pfam00037 159087004122 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 159087004123 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 159087004124 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 159087004125 quinone interaction residues [chemical binding]; other site 159087004126 active site 159087004127 catalytic residues [active] 159087004128 FMN binding site [chemical binding]; other site 159087004129 substrate binding site [chemical binding]; other site 159087004130 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 159087004131 macrolide transporter subunit MacA; Provisional; Region: PRK11578 159087004132 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087004133 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087004134 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087004135 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 159087004136 Walker A/P-loop; other site 159087004137 ATP binding site [chemical binding]; other site 159087004138 Q-loop/lid; other site 159087004139 ABC transporter signature motif; other site 159087004140 Walker B; other site 159087004141 D-loop; other site 159087004142 H-loop/switch region; other site 159087004143 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087004144 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087004145 FtsX-like permease family; Region: FtsX; pfam02687 159087004146 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 159087004147 TPR repeat; Region: TPR_11; pfam13414 159087004148 TPR repeat; Region: TPR_11; pfam13414 159087004149 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 159087004150 binding surface 159087004151 TPR motif; other site 159087004152 Tetratricopeptide repeat; Region: TPR_12; pfam13424 159087004153 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 159087004154 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 159087004155 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 159087004156 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 159087004157 dimer interface [polypeptide binding]; other site 159087004158 active site 159087004159 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 159087004160 Esterase/lipase [General function prediction only]; Region: COG1647 159087004161 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 159087004162 Outer membrane efflux protein; Region: OEP; pfam02321 159087004163 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087004164 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087004165 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087004166 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087004167 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087004168 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; pfam09849 159087004169 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 159087004170 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 159087004171 active site 159087004172 phosphorylation site [posttranslational modification] 159087004173 intermolecular recognition site; other site 159087004174 dimerization interface [polypeptide binding]; other site 159087004175 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 159087004176 DNA binding site [nucleotide binding] 159087004177 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 159087004178 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087004179 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 159087004180 dimer interface [polypeptide binding]; other site 159087004181 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 159087004182 ATP binding site [chemical binding]; other site 159087004183 Mg2+ binding site [ion binding]; other site 159087004184 G-X-G motif; other site 159087004185 Protein of unknown function, DUF; Region: DUF411; cl01142 159087004186 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 159087004187 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087004188 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 159087004189 potassium uptake protein; Region: kup; TIGR00794 159087004190 Acylphosphatases [Energy production and conversion]; Region: AcyP; COG1254 159087004191 Phytochelatin synthase; Region: Phytochelatin; pfam05023 159087004192 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 159087004193 Repair protein; Region: Repair_PSII; cl01535 159087004194 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 159087004195 Repair protein; Region: Repair_PSII; pfam04536 159087004196 LemA family; Region: LemA; pfam04011 159087004197 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 159087004198 putative active site [active] 159087004199 putative catalytic site [active] 159087004200 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 159087004201 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 159087004202 putative active site [active] 159087004203 putative metal binding site [ion binding]; other site 159087004204 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 159087004205 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 159087004206 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 159087004207 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 159087004208 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 159087004209 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 159087004210 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 159087004211 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 159087004212 Walker A/P-loop; other site 159087004213 ATP binding site [chemical binding]; other site 159087004214 Q-loop/lid; other site 159087004215 ABC transporter signature motif; other site 159087004216 Walker B; other site 159087004217 D-loop; other site 159087004218 H-loop/switch region; other site 159087004219 TOBE domain; Region: TOBE_2; pfam08402 159087004220 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 159087004221 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 159087004222 dimer interface [polypeptide binding]; other site 159087004223 conserved gate region; other site 159087004224 putative PBP binding loops; other site 159087004225 ABC-ATPase subunit interface; other site 159087004226 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 159087004227 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 159087004228 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087004229 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 159087004230 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 159087004231 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 159087004232 NlpC/P60 family; Region: NLPC_P60; pfam00877 159087004233 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 159087004234 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 159087004235 NADP binding site [chemical binding]; other site 159087004236 dimer interface [polypeptide binding]; other site 159087004237 Response regulator receiver domain; Region: Response_reg; pfam00072 159087004238 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 159087004239 active site 159087004240 phosphorylation site [posttranslational modification] 159087004241 intermolecular recognition site; other site 159087004242 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087004243 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087004244 metal binding site [ion binding]; metal-binding site 159087004245 active site 159087004246 I-site; other site 159087004247 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 159087004248 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087004249 acyl-activating enzyme (AAE) consensus motif; other site 159087004250 AMP binding site [chemical binding]; other site 159087004251 active site 159087004252 CoA binding site [chemical binding]; other site 159087004253 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 159087004254 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 159087004255 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 159087004256 Permease; Region: Permease; pfam02405 159087004257 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 159087004258 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087004259 Walker A/P-loop; other site 159087004260 ATP binding site [chemical binding]; other site 159087004261 Q-loop/lid; other site 159087004262 ABC transporter signature motif; other site 159087004263 Walker B; other site 159087004264 D-loop; other site 159087004265 H-loop/switch region; other site 159087004266 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 159087004267 mce related protein; Region: MCE; pfam02470 159087004268 Protein of unknown function (DUF330); Region: DUF330; cl01135 159087004269 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087004270 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087004271 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 159087004272 Ligand binding site [chemical binding]; other site 159087004273 Electron transfer flavoprotein domain; Region: ETF; pfam01012 159087004274 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 159087004275 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 159087004276 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 159087004277 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 159087004278 Predicted membrane protein [Function unknown]; Region: COG3235 159087004279 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 159087004280 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 159087004281 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 159087004282 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087004283 active site 159087004284 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 159087004285 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 159087004286 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 159087004287 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 159087004288 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 159087004289 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 159087004290 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 159087004291 replicative DNA helicase; Region: DnaB; TIGR00665 159087004292 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 159087004293 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 159087004294 Walker A motif; other site 159087004295 ATP binding site [chemical binding]; other site 159087004296 Walker B motif; other site 159087004297 DNA binding loops [nucleotide binding] 159087004298 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 159087004299 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 159087004300 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 159087004301 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 159087004302 putative active site [active] 159087004303 PhoH-like protein; Region: PhoH; pfam02562 159087004304 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 159087004305 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 159087004306 catalytic triad [active] 159087004307 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_18; cd08505 159087004308 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 159087004309 Methyltransferase domain; Region: Methyltransf_32; pfam13679 159087004310 phosphoglycolate phosphatase; Provisional; Region: PRK13222 159087004311 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 159087004312 motif II; other site 159087004313 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 159087004314 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 159087004315 S-adenosylmethionine binding site [chemical binding]; other site 159087004316 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087004317 ligand binding site [chemical binding]; other site 159087004318 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 159087004319 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 159087004320 active site 159087004321 putative substrate binding pocket [chemical binding]; other site 159087004322 DNA gyrase subunit A; Validated; Region: PRK05560 159087004323 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 159087004324 CAP-like domain; other site 159087004325 active site 159087004326 primary dimer interface [polypeptide binding]; other site 159087004327 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087004328 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087004329 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087004330 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087004331 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 159087004332 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 159087004333 homodimer interface [polypeptide binding]; other site 159087004334 substrate-cofactor binding pocket; other site 159087004335 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087004336 catalytic residue [active] 159087004337 Chorismate mutase type II; Region: CM_2; cl00693 159087004338 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 159087004339 Prephenate dehydratase; Region: PDT; pfam00800 159087004340 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 159087004341 putative L-Phe binding site [chemical binding]; other site 159087004342 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 159087004343 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 159087004344 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087004345 homodimer interface [polypeptide binding]; other site 159087004346 catalytic residue [active] 159087004347 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 159087004348 prephenate dehydrogenase; Validated; Region: PRK08507 159087004349 DNA ligase; Provisional; Region: PRK09125 159087004350 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 159087004351 DNA binding site [nucleotide binding] 159087004352 active site 159087004353 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 159087004354 DNA binding site [nucleotide binding] 159087004355 UDP-glucose 4-epimerase; Region: PLN02240 159087004356 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 159087004357 NAD binding site [chemical binding]; other site 159087004358 homodimer interface [polypeptide binding]; other site 159087004359 active site 159087004360 substrate binding site [chemical binding]; other site 159087004361 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 159087004362 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 159087004363 NAD binding site [chemical binding]; other site 159087004364 substrate binding site [chemical binding]; other site 159087004365 homodimer interface [polypeptide binding]; other site 159087004366 active site 159087004367 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 159087004368 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 159087004369 substrate binding site; other site 159087004370 tetramer interface; other site 159087004371 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 159087004372 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 159087004373 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 159087004374 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 159087004375 inhibitor-cofactor binding pocket; inhibition site 159087004376 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087004377 catalytic residue [active] 159087004378 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087004379 H-loop/switch region; other site 159087004380 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 159087004381 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 159087004382 active site 159087004383 catalytic tetrad [active] 159087004384 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 159087004385 ligand binding site; other site 159087004386 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 159087004387 glutamate-1-semialdehyde 2,1-aminomutase; Provisional; Region: PRK06209 159087004388 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087004389 catalytic residue [active] 159087004390 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 159087004391 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 159087004392 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 159087004393 Formyl transferase catalytic core domain found in a group of proteins with unknown functions; Region: FMT_core_like_1; cd08821 159087004394 putative active site [active] 159087004395 putative substrate binding site [chemical binding]; other site 159087004396 putative cosubstrate binding site; other site 159087004397 catalytic site [active] 159087004398 pseudaminic acid synthase; Region: PseI; TIGR03586 159087004399 NeuB family; Region: NeuB; pfam03102 159087004400 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 159087004401 NeuB binding interface [polypeptide binding]; other site 159087004402 putative substrate binding site [chemical binding]; other site 159087004403 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 159087004404 putative transferase, LIC12162 family; Region: o_ant_LIC12162; TIGR04331 159087004405 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 159087004406 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 159087004407 Methyltransferase domain; Region: Methyltransf_23; pfam13489 159087004408 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 159087004409 S-adenosylmethionine binding site [chemical binding]; other site 159087004410 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 159087004411 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004412 UDP-glucose 4-epimerase (G4E), subgroup 5, extended (e) SDRs; Region: UDP_G4E_5_SDR_e; cd05264 159087004413 putative NAD(P) binding site [chemical binding]; other site 159087004414 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 159087004415 active site 159087004416 putative substrate binding site [chemical binding]; other site 159087004417 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 159087004418 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 159087004419 substrate binding site; other site 159087004420 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 159087004421 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 159087004422 NAD binding site [chemical binding]; other site 159087004423 homotetramer interface [polypeptide binding]; other site 159087004424 homodimer interface [polypeptide binding]; other site 159087004425 substrate binding site [chemical binding]; other site 159087004426 active site 159087004427 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 159087004428 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004429 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 159087004430 NAD(P) binding site [chemical binding]; other site 159087004431 extended (e) SDRs; Region: SDR_e; cd08946 159087004432 NAD(P) binding site [chemical binding]; other site 159087004433 active site 159087004434 active site 159087004435 substrate binding site [chemical binding]; other site 159087004436 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 159087004437 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 159087004438 active site 159087004439 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004440 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 159087004441 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 159087004442 putative glycosyl transferase; Provisional; Region: PRK10307 159087004443 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 159087004444 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 159087004445 NADP binding site [chemical binding]; other site 159087004446 active site 159087004447 putative substrate binding site [chemical binding]; other site 159087004448 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 159087004449 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 159087004450 NAD(P) binding site [chemical binding]; other site 159087004451 homodimer interface [polypeptide binding]; other site 159087004452 substrate binding site [chemical binding]; other site 159087004453 active site 159087004454 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 159087004455 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 159087004456 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 159087004457 active site 159087004458 homodimer interface [polypeptide binding]; other site 159087004459 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004460 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 159087004461 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 159087004462 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which...; Region: GT_MraY_like; cd06912 159087004463 Mg++ binding site [ion binding]; other site 159087004464 putative catalytic motif [active] 159087004465 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 159087004466 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 159087004467 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 159087004468 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 159087004469 Probable Catalytic site; other site 159087004470 metal-binding site 159087004471 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004472 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 159087004473 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 159087004474 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 159087004475 active site 159087004476 dimer interface [polypeptide binding]; other site 159087004477 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 159087004478 Ligand Binding Site [chemical binding]; other site 159087004479 Molecular Tunnel; other site 159087004480 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 159087004481 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087004482 putative ADP-binding pocket [chemical binding]; other site 159087004483 Bacterial sugar transferase; Region: Bac_transf; pfam02397 159087004484 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 159087004485 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 159087004486 NAD(P) binding site [chemical binding]; other site 159087004487 homodimer interface [polypeptide binding]; other site 159087004488 substrate binding site [chemical binding]; other site 159087004489 active site 159087004490 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 159087004491 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 159087004492 hinge; other site 159087004493 active site 159087004494 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 159087004495 CMP-binding site; other site 159087004496 The sites determining sugar specificity; other site 159087004497 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 159087004498 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 159087004499 RNA binding site [nucleotide binding]; other site 159087004500 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 159087004501 RNA binding site [nucleotide binding]; other site 159087004502 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 159087004503 RNA binding site [nucleotide binding]; other site 159087004504 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 159087004505 RNA binding site [nucleotide binding]; other site 159087004506 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 159087004507 RNA binding site [nucleotide binding]; other site 159087004508 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 159087004509 RNA binding site [nucleotide binding]; other site 159087004510 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 159087004511 IHF dimer interface [polypeptide binding]; other site 159087004512 IHF - DNA interface [nucleotide binding]; other site 159087004513 Uncharacterized integral membrane protein [Function unknown]; Region: COG5416 159087004514 tetratricopeptide repeat protein; Provisional; Region: PRK11788 159087004515 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 159087004516 binding surface 159087004517 TPR motif; other site 159087004518 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 159087004519 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 159087004520 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 159087004521 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 159087004522 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 159087004523 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 159087004524 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 159087004525 putative ribose interaction site [chemical binding]; other site 159087004526 putative ADP binding site [chemical binding]; other site 159087004527 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 159087004528 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 159087004529 NADP binding site [chemical binding]; other site 159087004530 homopentamer interface [polypeptide binding]; other site 159087004531 substrate binding site [chemical binding]; other site 159087004532 active site 159087004533 cysteine synthase B; Region: cysM; TIGR01138 159087004534 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 159087004535 dimer interface [polypeptide binding]; other site 159087004536 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087004537 catalytic residue [active] 159087004538 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 159087004539 active site 159087004540 catalytic site [active] 159087004541 substrate binding site [chemical binding]; other site 159087004542 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 159087004543 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 159087004544 dimer interface [polypeptide binding]; other site 159087004545 substrate binding site [chemical binding]; other site 159087004546 metal binding sites [ion binding]; metal-binding site 159087004547 NAD synthetase; Provisional; Region: PRK13981 159087004548 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 159087004549 multimer interface [polypeptide binding]; other site 159087004550 active site 159087004551 catalytic triad [active] 159087004552 protein interface 1 [polypeptide binding]; other site 159087004553 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 159087004554 homodimer interface [polypeptide binding]; other site 159087004555 NAD binding pocket [chemical binding]; other site 159087004556 ATP binding pocket [chemical binding]; other site 159087004557 Mg binding site [ion binding]; other site 159087004558 active-site loop [active] 159087004559 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 159087004560 Nitrogen regulatory protein P-II; Region: P-II; smart00938 159087004561 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 159087004562 Smr domain; Region: Smr; pfam01713 159087004563 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 159087004564 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 159087004565 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 159087004566 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087004567 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 159087004568 ligand binding site [chemical binding]; other site 159087004569 flexible hinge region; other site 159087004570 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 159087004571 putative switch regulator; other site 159087004572 non-specific DNA interactions [nucleotide binding]; other site 159087004573 DNA binding site [nucleotide binding] 159087004574 sequence specific DNA binding site [nucleotide binding]; other site 159087004575 putative cAMP binding site [chemical binding]; other site 159087004576 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 159087004577 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 159087004578 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 159087004579 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 159087004580 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 159087004581 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 159087004582 putative uracil binding site [chemical binding]; other site 159087004583 putative active site [active] 159087004584 recombination factor protein RarA; Reviewed; Region: PRK13342 159087004585 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 159087004586 Walker A motif; other site 159087004587 ATP binding site [chemical binding]; other site 159087004588 Walker B motif; other site 159087004589 arginine finger; other site 159087004590 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 159087004591 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 159087004592 seryl-tRNA synthetase; Provisional; Region: PRK05431 159087004593 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 159087004594 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 159087004595 dimer interface [polypeptide binding]; other site 159087004596 active site 159087004597 motif 1; other site 159087004598 motif 2; other site 159087004599 motif 3; other site 159087004600 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 159087004601 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 159087004602 substrate binding pocket [chemical binding]; other site 159087004603 membrane-bound complex binding site; other site 159087004604 hinge residues; other site 159087004605 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 159087004606 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087004607 catalytic residue [active] 159087004608 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 159087004609 INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinases and phage-related integrases. Some have N-terminal domains, which show little sequence...; Region: INT_SG2_C; cd01184 159087004610 Int/Topo IB signature motif; other site 159087004611 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 159087004612 HsdM N-terminal domain; Region: HsdM_N; pfam12161 159087004613 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 159087004614 S-adenosylmethionine binding site [chemical binding]; other site 159087004615 putative transposase OrfB; Reviewed; Region: PHA02517 159087004616 HTH-like domain; Region: HTH_21; pfam13276 159087004617 Integrase core domain; Region: rve; pfam00665 159087004618 Integrase core domain; Region: rve_3; pfam13683 159087004619 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 159087004620 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 159087004621 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 159087004622 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 159087004623 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 159087004624 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 159087004625 ATP binding site [chemical binding]; other site 159087004626 putative Mg++ binding site [ion binding]; other site 159087004627 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 159087004628 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087004629 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 159087004630 ATP binding site [chemical binding]; other site 159087004631 putative Mg++ binding site [ion binding]; other site 159087004632 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 159087004633 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 159087004634 non-specific DNA binding site [nucleotide binding]; other site 159087004635 salt bridge; other site 159087004636 sequence-specific DNA binding site [nucleotide binding]; other site 159087004637 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 159087004638 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 159087004639 catalytic residues [active] 159087004640 catalytic nucleophile [active] 159087004641 Presynaptic Site I dimer interface [polypeptide binding]; other site 159087004642 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 159087004643 Synaptic Flat tetramer interface [polypeptide binding]; other site 159087004644 Synaptic Site I dimer interface [polypeptide binding]; other site 159087004645 DNA binding site [nucleotide binding] 159087004646 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 159087004647 DNA-binding interface [nucleotide binding]; DNA binding site 159087004648 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 159087004649 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 159087004650 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 159087004651 dimer interface [polypeptide binding]; other site 159087004652 putative PBP binding loops; other site 159087004653 ABC-ATPase subunit interface; other site 159087004654 antimicrobial peptide ABC transporter permease SapC; Provisional; Region: PRK15111 159087004655 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 159087004656 dimer interface [polypeptide binding]; other site 159087004657 conserved gate region; other site 159087004658 putative PBP binding loops; other site 159087004659 ABC-ATPase subunit interface; other site 159087004660 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 159087004661 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 159087004662 Walker A/P-loop; other site 159087004663 ATP binding site [chemical binding]; other site 159087004664 Q-loop/lid; other site 159087004665 ABC transporter signature motif; other site 159087004666 Walker B; other site 159087004667 D-loop; other site 159087004668 H-loop/switch region; other site 159087004669 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 159087004670 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 159087004671 Walker A/P-loop; other site 159087004672 ATP binding site [chemical binding]; other site 159087004673 Q-loop/lid; other site 159087004674 ABC transporter signature motif; other site 159087004675 Walker B; other site 159087004676 D-loop; other site 159087004677 H-loop/switch region; other site 159087004678 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 159087004679 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 159087004680 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087004681 catalytic residue [active] 159087004682 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 159087004683 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 159087004684 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 159087004685 active site 159087004686 HIGH motif; other site 159087004687 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 159087004688 active site 159087004689 KMSKS motif; other site 159087004690 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 159087004691 non-specific DNA binding site [nucleotide binding]; other site 159087004692 salt bridge; other site 159087004693 sequence-specific DNA binding site [nucleotide binding]; other site 159087004694 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 159087004695 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 159087004696 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 159087004697 active site 159087004698 DNA binding site [nucleotide binding] 159087004699 Int/Topo IB signature motif; other site 159087004700 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087004701 Zn2+ binding site [ion binding]; other site 159087004702 Mg2+ binding site [ion binding]; other site 159087004703 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 159087004704 IHF dimer interface [polypeptide binding]; other site 159087004705 IHF - DNA interface [nucleotide binding]; other site 159087004706 Restriction endonuclease; Region: Mrr_cat; pfam04471 159087004707 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087004708 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 159087004709 active site 159087004710 phosphorylation site [posttranslational modification] 159087004711 intermolecular recognition site; other site 159087004712 dimerization interface [polypeptide binding]; other site 159087004713 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087004714 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 159087004715 MarR family; Region: MarR_2; cl17246 159087004716 Hemerythrin; Region: Hemerythrin; cd12107 159087004717 Fe binding site [ion binding]; other site 159087004718 Lipocalin-like domain; Region: Lipocalin_5; pfam13924 159087004719 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 159087004720 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 159087004721 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 159087004722 active site 159087004723 Fe binding site [ion binding]; other site 159087004724 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 159087004725 Ligand Binding Site [chemical binding]; other site 159087004726 indole acetimide hydrolase; Validated; Region: PRK07488 159087004727 Amidase; Region: Amidase; cl11426 159087004728 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 159087004729 putative metal binding site [ion binding]; other site 159087004730 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 159087004731 dimer interface [polypeptide binding]; other site 159087004732 FMN binding site [chemical binding]; other site 159087004733 Domain of unknown function (DUF336); Region: DUF336; pfam03928 159087004734 Uncharacterized conserved protein [Function unknown]; Region: COG1359 159087004735 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 159087004736 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 159087004737 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 159087004738 Cupin domain; Region: Cupin_2; pfam07883 159087004739 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 159087004740 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 159087004741 NAD(P) binding site [chemical binding]; other site 159087004742 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 159087004743 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 159087004744 Protein export membrane protein; Region: SecD_SecF; cl14618 159087004745 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 159087004746 Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), which catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate; Region: MhpB_like; cd07365 159087004747 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 159087004748 putative active site [active] 159087004749 Fe(II) binding site [ion binding]; other site 159087004750 putative dimer interface [polypeptide binding]; other site 159087004751 putative tetramer interface [polypeptide binding]; other site 159087004752 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087004753 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087004754 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 159087004755 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087004756 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087004757 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087004758 active site 159087004759 catalytic residues [active] 159087004760 metal binding site [ion binding]; metal-binding site 159087004761 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087004762 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 159087004763 classical (c) SDRs; Region: SDR_c; cd05233 159087004764 NAD(P) binding site [chemical binding]; other site 159087004765 active site 159087004766 Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating...; Region: Rieske_RO_Alpha_OMO_CARDO; cd03548 159087004767 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 159087004768 iron-sulfur cluster [ion binding]; other site 159087004769 alpha subunit interaction site [polypeptide binding]; other site 159087004770 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 159087004771 alpha subunit interface [polypeptide binding]; other site 159087004772 active site 159087004773 substrate binding site [chemical binding]; other site 159087004774 Fe binding site [ion binding]; other site 159087004775 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087004776 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 159087004777 catalytic loop [active] 159087004778 iron binding site [ion binding]; other site 159087004779 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 159087004780 FAD binding pocket [chemical binding]; other site 159087004781 FAD binding motif [chemical binding]; other site 159087004782 phosphate binding motif [ion binding]; other site 159087004783 beta-alpha-beta structure motif; other site 159087004784 NAD binding pocket [chemical binding]; other site 159087004785 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 159087004786 Amidase; Region: Amidase; pfam01425 159087004787 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087004788 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 159087004789 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 159087004790 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 159087004791 putative active site [active] 159087004792 heme pocket [chemical binding]; other site 159087004793 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 159087004794 putative active site [active] 159087004795 heme pocket [chemical binding]; other site 159087004796 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087004797 metal binding site [ion binding]; metal-binding site 159087004798 active site 159087004799 I-site; other site 159087004800 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 159087004801 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 159087004802 PAS domain; Region: PAS_9; pfam13426 159087004803 putative active site [active] 159087004804 heme pocket [chemical binding]; other site 159087004805 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087004806 dimer interface [polypeptide binding]; other site 159087004807 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 159087004808 putative CheW interface [polypeptide binding]; other site 159087004809 T5orf172 domain; Region: T5orf172; pfam10544 159087004810 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; Region: Sig-70_plancto1; TIGR02984 159087004811 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087004812 DNA-binding HTH domain-containing proteins [Transcription]; Region: CsgD; COG2771 159087004813 DNA binding residues [nucleotide binding] 159087004814 dimerization interface [polypeptide binding]; other site 159087004815 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 159087004816 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 159087004817 TIGR02594 family protein; Region: TIGR02594 159087004818 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 159087004819 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 159087004820 Transposase; Region: DEDD_Tnp_IS110; pfam01548 159087004821 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 159087004822 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 159087004823 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 159087004824 active site 159087004825 catalytic residues [active] 159087004826 Int/Topo IB signature motif; other site 159087004827 DNA binding site [nucleotide binding] 159087004828 Uncharacterized conserved protein [Function unknown]; Region: COG1739 159087004829 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 159087004830 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 159087004831 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 159087004832 active site 159087004833 catalytic site [active] 159087004834 substrate binding site [chemical binding]; other site 159087004835 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 159087004836 GST_N family, Omega-like subfamily; composed of uncharacterized proteins with similarity to class Omega 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_Omega_like; cd03060 159087004837 putative GSH binding site (G-site) [chemical binding]; other site 159087004838 active site cysteine [active] 159087004839 putative C-terminal domain interface [polypeptide binding]; other site 159087004840 putative dimer interface [polypeptide binding]; other site 159087004841 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 159087004842 putative N-terminal domain interface [polypeptide binding]; other site 159087004843 putative dimer interface [polypeptide binding]; other site 159087004844 putative substrate binding pocket (H-site) [chemical binding]; other site 159087004845 RNAse HI family that includes Archaeal RNase HI; Region: RNase_HI_archaeal_like; cd09279 159087004846 RNA/DNA hybrid binding site [nucleotide binding]; other site 159087004847 active site 159087004848 LTXXQ motif family protein; Region: LTXXQ; pfam07813 159087004849 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 159087004850 DNA-binding site [nucleotide binding]; DNA binding site 159087004851 RNA-binding motif; other site 159087004852 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 159087004853 active site residue [active] 159087004854 Pirin-related protein [General function prediction only]; Region: COG1741 159087004855 Pirin; Region: Pirin; pfam02678 159087004856 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 159087004857 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 159087004858 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 159087004859 LysR family transcriptional regulator; Provisional; Region: PRK14997 159087004860 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087004861 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 159087004862 putative effector binding pocket; other site 159087004863 dimerization interface [polypeptide binding]; other site 159087004864 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 159087004865 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 159087004866 NifZ domain; Region: NifZ; pfam04319 159087004867 Nitrogen fixation protein NifW; Region: NifW; pfam03206 159087004868 serine O-acetyltransferase; Region: cysE; TIGR01172 159087004869 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 159087004870 trimer interface [polypeptide binding]; other site 159087004871 active site 159087004872 substrate binding site [chemical binding]; other site 159087004873 CoA binding site [chemical binding]; other site 159087004874 homocitrate synthase NifV; Region: nifV_homocitr; TIGR02660 159087004875 Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_NifV; cd07939 159087004876 active site 159087004877 catalytic residues [active] 159087004878 metal binding site [ion binding]; metal-binding site 159087004879 PAS domain S-box; Region: sensory_box; TIGR00229 159087004880 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 159087004881 putative active site [active] 159087004882 heme pocket [chemical binding]; other site 159087004883 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 159087004884 Histidine kinase; Region: HisKA_3; pfam07730 159087004885 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 159087004886 ATP binding site [chemical binding]; other site 159087004887 Mg2+ binding site [ion binding]; other site 159087004888 G-X-G motif; other site 159087004889 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087004890 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 159087004891 active site 159087004892 phosphorylation site [posttranslational modification] 159087004893 intermolecular recognition site; other site 159087004894 dimerization interface [polypeptide binding]; other site 159087004895 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 159087004896 DNA binding residues [nucleotide binding] 159087004897 dimerization interface [polypeptide binding]; other site 159087004898 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 159087004899 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 159087004900 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 159087004901 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 159087004902 decaheme-associated outer membrane protein, MtrB/PioB family; Region: OMP_MtrB_PioB; TIGR03509 159087004903 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 159087004904 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 159087004905 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 159087004906 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 159087004907 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 159087004908 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 159087004909 TPR repeat; Region: TPR_11; pfam13414 159087004910 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 159087004911 binding surface 159087004912 TPR motif; other site 159087004913 Hemerythrin; Region: Hemerythrin; cd12107 159087004914 Fe binding site [ion binding]; other site 159087004915 LRV protein FeS4 cluster; Region: LRV_FeS; pfam05484 159087004916 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 159087004917 HEAT repeats; Region: HEAT_2; pfam13646 159087004918 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 159087004919 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 159087004920 NifT/FixU protein; Region: NifT; pfam06988 159087004921 nitrogenase molybdenum-iron protein beta chain; Region: nifK; TIGR01286 159087004922 Domain of unknown function (DUF3364); Region: DUF3364; pfam11844 159087004923 Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems; Region: Nitrogenase_MoFe_beta; cd01974 159087004924 MoFe protein beta/alpha subunit interactions; other site 159087004925 Beta subunit P cluster binding residues; other site 159087004926 MoFe protein beta subunit/Fe protein contacts; other site 159087004927 MoFe protein dimer/ dimer interactions; other site 159087004928 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 159087004929 Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to...; Region: Nitrogenase_MoFe_alpha; cd01976 159087004930 MoFe protein alpha/beta subunit interactions; other site 159087004931 Alpha subunit P cluster binding residues; other site 159087004932 FeMoco binding residues [chemical binding]; other site 159087004933 MoFe protein alpha subunit/Fe protein contacts; other site 159087004934 MoFe protein dimer/ dimer interactions; other site 159087004935 NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the...; Region: NifH; cd02040 159087004936 nitrogenase iron protein; Region: nifH; TIGR01287 159087004937 Nucleotide-binding sites [chemical binding]; other site 159087004938 Walker A motif; other site 159087004939 Switch I region of nucleotide binding site; other site 159087004940 Fe4S4 binding sites [ion binding]; other site 159087004941 Switch II region of nucleotide binding site; other site 159087004942 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 159087004943 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 159087004944 Hemerythrin; Region: Hemerythrin; cd12107 159087004945 Fe binding site [ion binding]; other site 159087004946 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 159087004947 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 159087004948 NADPH bind site [chemical binding]; other site 159087004949 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 159087004950 putative FMN binding site [chemical binding]; other site 159087004951 NADPH bind site [chemical binding]; other site 159087004952 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 159087004953 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087004954 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 159087004955 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 159087004956 UreF; Region: UreF; pfam01730 159087004957 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 159087004958 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 159087004959 dimer interface [polypeptide binding]; other site 159087004960 catalytic residues [active] 159087004961 urease subunit alpha; Reviewed; Region: ureC; PRK13207 159087004962 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 159087004963 subunit interactions [polypeptide binding]; other site 159087004964 active site 159087004965 flap region; other site 159087004966 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 159087004967 alpha-beta subunit interface [polypeptide binding]; other site 159087004968 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 159087004969 alpha-gamma subunit interface [polypeptide binding]; other site 159087004970 beta-gamma subunit interface [polypeptide binding]; other site 159087004971 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 159087004972 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 159087004973 Coenzyme A binding pocket [chemical binding]; other site 159087004974 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 159087004975 S-adenosylmethionine binding site [chemical binding]; other site 159087004976 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 159087004977 Helix-turn-helix domain; Region: HTH_38; pfam13936 159087004978 Homeodomain-like domain; Region: HTH_32; pfam13565 159087004979 Integrase core domain; Region: rve; pfam00665 159087004980 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 159087004981 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087004982 Walker A/P-loop; other site 159087004983 ATP binding site [chemical binding]; other site 159087004984 Q-loop/lid; other site 159087004985 ABC transporter signature motif; other site 159087004986 Walker B; other site 159087004987 D-loop; other site 159087004988 H-loop/switch region; other site 159087004989 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 159087004990 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087004991 Walker A/P-loop; other site 159087004992 ATP binding site [chemical binding]; other site 159087004993 Q-loop/lid; other site 159087004994 ABC transporter signature motif; other site 159087004995 Walker B; other site 159087004996 D-loop; other site 159087004997 H-loop/switch region; other site 159087004998 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087004999 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087005000 TM-ABC transporter signature motif; other site 159087005001 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087005002 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 159087005003 TM-ABC transporter signature motif; other site 159087005004 Nitrogen fixation protein of unknown function; Region: Nif11; pfam07862 159087005005 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 159087005006 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 159087005007 ligand binding site [chemical binding]; other site 159087005008 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 159087005009 dimerization interface [polypeptide binding]; other site 159087005010 PAS fold; Region: PAS_4; pfam08448 159087005011 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 159087005012 putative active site [active] 159087005013 heme pocket [chemical binding]; other site 159087005014 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 159087005015 dimer interface [polypeptide binding]; other site 159087005016 phosphorylation site [posttranslational modification] 159087005017 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 159087005018 ATP binding site [chemical binding]; other site 159087005019 Mg2+ binding site [ion binding]; other site 159087005020 G-X-G motif; other site 159087005021 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005022 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 159087005023 active site 159087005024 phosphorylation site [posttranslational modification] 159087005025 intermolecular recognition site; other site 159087005026 dimerization interface [polypeptide binding]; other site 159087005027 cyanate hydratase; Validated; Region: PRK02866 159087005028 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 159087005029 oligomer interface [polypeptide binding]; other site 159087005030 active site 159087005031 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 159087005032 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 159087005033 putative ligand binding site [chemical binding]; other site 159087005034 phosphoglucomutase; Validated; Region: PRK07564 159087005035 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 159087005036 active site 159087005037 substrate binding site [chemical binding]; other site 159087005038 metal binding site [ion binding]; metal-binding site 159087005039 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005040 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 159087005041 active site 159087005042 phosphorylation site [posttranslational modification] 159087005043 intermolecular recognition site; other site 159087005044 dimerization interface [polypeptide binding]; other site 159087005045 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 159087005046 DNA binding residues [nucleotide binding] 159087005047 dimerization interface [polypeptide binding]; other site 159087005048 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 159087005049 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 159087005050 Na binding site [ion binding]; other site 159087005051 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087005052 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 159087005053 dimer interface [polypeptide binding]; other site 159087005054 phosphorylation site [posttranslational modification] 159087005055 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 159087005056 ATP binding site [chemical binding]; other site 159087005057 Mg2+ binding site [ion binding]; other site 159087005058 G-X-G motif; other site 159087005059 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005060 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 159087005061 active site 159087005062 phosphorylation site [posttranslational modification] 159087005063 intermolecular recognition site; other site 159087005064 dimerization interface [polypeptide binding]; other site 159087005065 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 159087005066 NifQ; Region: NifQ; pfam04891 159087005067 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 159087005068 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 159087005069 catalytic loop [active] 159087005070 iron binding site [ion binding]; other site 159087005071 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 159087005072 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 159087005073 catalytic loop [active] 159087005074 iron binding site [ion binding]; other site 159087005075 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 159087005076 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087005077 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 159087005078 Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also...; Region: ArsC_15kD; cd03033 159087005079 putative catalytic residues [active] 159087005080 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087005081 4Fe-4S binding domain; Region: Fer4; cl02805 159087005082 nitrogenase cofactor biosynthesis protein NifB; Region: nifB; TIGR01290 159087005083 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 159087005084 FeS/SAM binding site; other site 159087005085 NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of...; Region: NifB; cd00852 159087005086 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 159087005087 flavodoxin FldA; Validated; Region: PRK09267 159087005088 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 159087005089 active site residue [active] 159087005090 PEP-CTERM motif; Region: VPEP; pfam07589 159087005091 Protein of unknown function (DUF550); Region: DUF550; pfam04447 159087005092 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 159087005093 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 159087005094 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 159087005095 UbiA prenyltransferase family; Region: UbiA; pfam01040 159087005096 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 159087005097 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 159087005098 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 159087005099 Subunit III/VIIa interface [polypeptide binding]; other site 159087005100 Phospholipid binding site [chemical binding]; other site 159087005101 Subunit I/III interface [polypeptide binding]; other site 159087005102 Subunit III/VIb interface [polypeptide binding]; other site 159087005103 Subunit III/VIa interface; other site 159087005104 Subunit III/Vb interface [polypeptide binding]; other site 159087005105 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 159087005106 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 159087005107 Subunit I/III interface [polypeptide binding]; other site 159087005108 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 159087005109 D-pathway; other site 159087005110 Subunit I/VIIc interface [polypeptide binding]; other site 159087005111 Subunit I/IV interface [polypeptide binding]; other site 159087005112 Subunit I/II interface [polypeptide binding]; other site 159087005113 Low-spin heme (heme a) binding site [chemical binding]; other site 159087005114 Subunit I/VIIa interface [polypeptide binding]; other site 159087005115 Subunit I/VIa interface [polypeptide binding]; other site 159087005116 Dimer interface; other site 159087005117 Putative water exit pathway; other site 159087005118 Binuclear center (heme a3/CuB) [ion binding]; other site 159087005119 K-pathway; other site 159087005120 Subunit I/Vb interface [polypeptide binding]; other site 159087005121 Putative proton exit pathway; other site 159087005122 Subunit I/VIb interface; other site 159087005123 Subunit I/VIc interface [polypeptide binding]; other site 159087005124 Electron transfer pathway; other site 159087005125 Subunit I/VIIIb interface [polypeptide binding]; other site 159087005126 Subunit I/VIIb interface [polypeptide binding]; other site 159087005127 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 159087005128 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 159087005129 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 159087005130 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087005131 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 159087005132 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 159087005133 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 159087005134 Cu(I) binding site [ion binding]; other site 159087005135 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 159087005136 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cl00252 159087005137 ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and...; Region: modD_like; cd01573 159087005138 molybdenum transport protein ModD; Provisional; Region: PRK06096 159087005139 dimerization interface [polypeptide binding]; other site 159087005140 active site 159087005141 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 159087005142 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 159087005143 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 159087005144 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 159087005145 molybdenum-pterin binding domain; Region: Mop; TIGR00638 159087005146 molybdenum-pterin binding domain; Region: Mop; TIGR00638 159087005147 molybdenum-pterin binding domain; Region: Mop; TIGR00638 159087005148 molybdenum-pterin binding domain; Region: Mop; TIGR00638 159087005149 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 159087005150 flavodoxin FldA; Validated; Region: PRK09267 159087005151 NifZ domain; Region: NifZ; pfam04319 159087005152 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 159087005153 dimer interface [polypeptide binding]; other site 159087005154 [2Fe-2S] cluster binding site [ion binding]; other site 159087005155 Nif-specific regulatory protein; Region: nifA; TIGR01817 159087005156 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 159087005157 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 159087005158 Walker A motif; other site 159087005159 ATP binding site [chemical binding]; other site 159087005160 Walker B motif; other site 159087005161 arginine finger; other site 159087005162 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087005163 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 159087005164 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 159087005165 putative active site [active] 159087005166 heme pocket [chemical binding]; other site 159087005167 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 159087005168 ATP binding site [chemical binding]; other site 159087005169 Mg2+ binding site [ion binding]; other site 159087005170 G-X-G motif; other site 159087005171 electron transport complex, RnfABCDGE type, G subunit; Region: rnfG; TIGR01947 159087005172 electron transport complex RsxE subunit; Provisional; Region: PRK12405 159087005173 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 159087005174 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 159087005175 electron transport complex protein RnfB; Provisional; Region: PRK05113 159087005176 4Fe-4S binding domain; Region: Fer4; pfam00037 159087005177 4Fe-4S binding domain; Region: Fer4; cl02805 159087005178 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 159087005179 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 159087005180 SLBB domain; Region: SLBB; pfam10531 159087005181 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 159087005182 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 159087005183 RnfH family Ubiquitin; Region: Ub-RnfH; pfam03658 159087005184 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 159087005185 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 159087005186 ligand binding site [chemical binding]; other site 159087005187 homodimer interface [polypeptide binding]; other site 159087005188 NAD(P) binding site [chemical binding]; other site 159087005189 trimer interface B [polypeptide binding]; other site 159087005190 trimer interface A [polypeptide binding]; other site 159087005191 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 159087005192 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 159087005193 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 159087005194 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 159087005195 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 159087005196 Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifE_I; cd01968 159087005197 choice-of-anchor C domain; Region: choice_anch_C; TIGR04362 159087005198 legume lectins; Region: lectin_L-type; cd01951 159087005199 homotetramer interaction site [polypeptide binding]; other site 159087005200 homodimer interaction site [polypeptide binding]; other site 159087005201 carbohydrate binding site [chemical binding]; other site 159087005202 metal binding site [ion binding]; metal-binding site 159087005203 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifN_1; cd01966 159087005204 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 159087005205 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 159087005206 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 159087005207 probable nitrogen fixation protein; Region: TIGR02935 159087005208 Rop-like; Region: Rop-like; pfam05082 159087005209 ferredoxin III, nif-specific; Region: fdxN_nitrog; TIGR02936 159087005210 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 159087005211 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 159087005212 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 159087005213 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 159087005214 trimerization site [polypeptide binding]; other site 159087005215 active site 159087005216 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 159087005217 NifU-like domain; Region: NifU; pfam01106 159087005218 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 159087005219 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 159087005220 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087005221 catalytic residue [active] 159087005222 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 159087005223 bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they...; Region: bact_SO_family_Moco; cd02108 159087005224 Moco binding site; other site 159087005225 metal coordination site [ion binding]; other site 159087005226 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 159087005227 RNA polymerase sigma factor; Provisional; Region: PRK12536 159087005228 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087005229 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 159087005230 DNA binding residues [nucleotide binding] 159087005231 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 159087005232 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 159087005233 SnoaL-like domain; Region: SnoaL_2; pfam12680 159087005234 Predicted flavin-nucleotide-binding protein structurally related to pyridoxine 5'-phosphate oxidase [General function prediction only]; Region: COG3576 159087005235 Uncharacterized conserved protein [Function unknown]; Region: COG2128 159087005236 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 159087005237 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087005238 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087005239 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_2; cd08471 159087005240 putative effector binding pocket; other site 159087005241 putative dimerization interface [polypeptide binding]; other site 159087005242 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 159087005243 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 159087005244 NADP binding site [chemical binding]; other site 159087005245 dimer interface [polypeptide binding]; other site 159087005246 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087005247 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087005248 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087005249 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_1; cd08460 159087005250 putative substrate binding pocket [chemical binding]; other site 159087005251 putative dimerization interface [polypeptide binding]; other site 159087005252 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 159087005253 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 159087005254 putative substrate translocation pore; other site 159087005255 C-20 methyltransferase BchU; Region: C20_methyl_CrtF; TIGR02716 159087005256 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 159087005257 S-adenosylmethionine binding site [chemical binding]; other site 159087005258 Phasin protein; Region: Phasin_2; pfam09361 159087005259 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 159087005260 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 159087005261 FAD binding pocket [chemical binding]; other site 159087005262 FAD binding motif [chemical binding]; other site 159087005263 phosphate binding motif [ion binding]; other site 159087005264 beta-alpha-beta structure motif; other site 159087005265 NAD binding pocket [chemical binding]; other site 159087005266 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 159087005267 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087005268 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 159087005269 putative dimerization interface [polypeptide binding]; other site 159087005270 Dihydroneopterin aldolase; Region: FolB; pfam02152 159087005271 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 159087005272 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 159087005273 folate binding site [chemical binding]; other site 159087005274 NADP+ binding site [chemical binding]; other site 159087005275 PAS fold; Region: PAS_3; pfam08447 159087005276 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 159087005277 PAS domain; Region: PAS_9; pfam13426 159087005278 putative active site [active] 159087005279 heme pocket [chemical binding]; other site 159087005280 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087005281 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005282 metal binding site [ion binding]; metal-binding site 159087005283 active site 159087005284 I-site; other site 159087005285 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 159087005286 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087005287 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087005288 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 159087005289 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087005290 active site 159087005291 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 159087005292 acetyl-CoA acetyltransferase; Provisional; Region: PRK08170 159087005293 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 159087005294 dimer interface [polypeptide binding]; other site 159087005295 active site 159087005296 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DegV; COG1307 159087005297 ERCC4 domain; Region: ERCC4; cl10594 159087005298 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 159087005299 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 159087005300 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 159087005301 substrate binding site [chemical binding]; other site 159087005302 oxyanion hole (OAH) forming residues; other site 159087005303 trimer interface [polypeptide binding]; other site 159087005304 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 159087005305 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 159087005306 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087005307 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 159087005308 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 159087005309 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 159087005310 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087005311 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 159087005312 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 159087005313 substrate binding site [chemical binding]; other site 159087005314 oxyanion hole (OAH) forming residues; other site 159087005315 trimer interface [polypeptide binding]; other site 159087005316 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 159087005317 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 159087005318 dimer interface [polypeptide binding]; other site 159087005319 active site 159087005320 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 159087005321 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 159087005322 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 159087005323 acyl-activating enzyme (AAE) consensus motif; other site 159087005324 putative AMP binding site [chemical binding]; other site 159087005325 putative active site [active] 159087005326 putative CoA binding site [chemical binding]; other site 159087005327 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 159087005328 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 159087005329 FMN binding site [chemical binding]; other site 159087005330 substrate binding site [chemical binding]; other site 159087005331 putative catalytic residue [active] 159087005332 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 159087005333 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 159087005334 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087005335 active site 159087005336 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 159087005337 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 159087005338 binding surface 159087005339 Tetratricopeptide repeat; Region: TPR_16; pfam13432 159087005340 TPR motif; other site 159087005341 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 159087005342 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 159087005343 PAS domain; Region: PAS; smart00091 159087005344 PAS fold; Region: PAS_4; pfam08448 159087005345 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087005346 Zn2+ binding site [ion binding]; other site 159087005347 Mg2+ binding site [ion binding]; other site 159087005348 Immunity protein Imm3; Region: Imm3; pfam14425 159087005349 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 159087005350 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 159087005351 catalytic residues [active] 159087005352 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 159087005353 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 159087005354 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 159087005355 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 159087005356 Walker A/P-loop; other site 159087005357 ATP binding site [chemical binding]; other site 159087005358 Q-loop/lid; other site 159087005359 ABC transporter signature motif; other site 159087005360 Walker B; other site 159087005361 D-loop; other site 159087005362 H-loop/switch region; other site 159087005363 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 159087005364 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087005365 4Fe-4S binding domain; Region: Fer4; pfam00037 159087005366 4Fe-4S dicluster domain; Region: Fer4_18; pfam13746 159087005367 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087005368 4Fe-4S binding domain; Region: Fer4; pfam00037 159087005369 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 159087005370 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 159087005371 Cytochrome c; Region: Cytochrom_C; cl11414 159087005372 Cytochrome c; Region: Cytochrom_C; cl11414 159087005373 Cytochrome c553 [Energy production and conversion]; Region: COG2863 159087005374 nitrous-oxide reductase, Sec-dependent; Region: nitrous_NosZ_Gp; TIGR04246 159087005375 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 159087005376 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087005377 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 159087005378 active site 159087005379 phosphorylation site [posttranslational modification] 159087005380 intermolecular recognition site; other site 159087005381 dimerization interface [polypeptide binding]; other site 159087005382 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 159087005383 DNA binding residues [nucleotide binding] 159087005384 dimerization interface [polypeptide binding]; other site 159087005385 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005386 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 159087005387 active site 159087005388 phosphorylation site [posttranslational modification] 159087005389 intermolecular recognition site; other site 159087005390 dimerization interface [polypeptide binding]; other site 159087005391 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 159087005392 Histidine kinase; Region: HisKA_3; pfam07730 159087005393 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 159087005394 ATP binding site [chemical binding]; other site 159087005395 Mg2+ binding site [ion binding]; other site 159087005396 G-X-G motif; other site 159087005397 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087005398 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087005399 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 159087005400 putative active site [active] 159087005401 heme pocket [chemical binding]; other site 159087005402 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 159087005403 dimer interface [polypeptide binding]; other site 159087005404 phosphorylation site [posttranslational modification] 159087005405 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 159087005406 ATP binding site [chemical binding]; other site 159087005407 Mg2+ binding site [ion binding]; other site 159087005408 G-X-G motif; other site 159087005409 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005410 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 159087005411 active site 159087005412 phosphorylation site [posttranslational modification] 159087005413 intermolecular recognition site; other site 159087005414 dimerization interface [polypeptide binding]; other site 159087005415 nitrous-oxide reductase, Sec-dependent; Region: nitrous_NosZ_Gp; TIGR04246 159087005416 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 159087005417 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 159087005418 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 159087005419 Cu(I) binding site [ion binding]; other site 159087005420 Protein of unknown function (DUF461); Region: DUF461; pfam04314 159087005421 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 159087005422 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087005423 putative active site [active] 159087005424 heme pocket [chemical binding]; other site 159087005425 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 159087005426 putative active site [active] 159087005427 heme pocket [chemical binding]; other site 159087005428 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087005429 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 159087005430 putative active site [active] 159087005431 heme pocket [chemical binding]; other site 159087005432 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 159087005433 putative active site [active] 159087005434 heme pocket [chemical binding]; other site 159087005435 PAS domain S-box; Region: sensory_box; TIGR00229 159087005436 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 159087005437 putative active site [active] 159087005438 heme pocket [chemical binding]; other site 159087005439 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087005440 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005441 metal binding site [ion binding]; metal-binding site 159087005442 active site 159087005443 I-site; other site 159087005444 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 159087005445 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 159087005446 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087005447 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 159087005448 dimer interface [polypeptide binding]; other site 159087005449 phosphorylation site [posttranslational modification] 159087005450 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 159087005451 ATP binding site [chemical binding]; other site 159087005452 Mg2+ binding site [ion binding]; other site 159087005453 G-X-G motif; other site 159087005454 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 159087005455 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 159087005456 active site 159087005457 phosphorylation site [posttranslational modification] 159087005458 intermolecular recognition site; other site 159087005459 dimerization interface [polypeptide binding]; other site 159087005460 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 159087005461 DNA binding site [nucleotide binding] 159087005462 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 159087005463 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 159087005464 Cytochrome c; Region: Cytochrom_C; cl11414 159087005465 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 159087005466 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 159087005467 active site 159087005468 phosphorylation site [posttranslational modification] 159087005469 intermolecular recognition site; other site 159087005470 dimerization interface [polypeptide binding]; other site 159087005471 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087005472 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087005473 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 159087005474 dimer interface [polypeptide binding]; other site 159087005475 phosphorylation site [posttranslational modification] 159087005476 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 159087005477 ATP binding site [chemical binding]; other site 159087005478 Mg2+ binding site [ion binding]; other site 159087005479 G-X-G motif; other site 159087005480 Cytochrome c; Region: Cytochrom_C; cl11414 159087005481 Cytochrome c; Region: Cytochrom_C; pfam00034 159087005482 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 159087005483 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 159087005484 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 159087005485 active site 159087005486 metal binding site [ion binding]; metal-binding site 159087005487 PGAP1-like protein; Region: PGAP1; pfam07819 159087005488 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087005489 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 159087005490 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 159087005491 active site 159087005492 catalytic site [active] 159087005493 substrate binding site [chemical binding]; other site 159087005494 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 159087005495 RNA/DNA hybrid binding site [nucleotide binding]; other site 159087005496 active site 159087005497 Methyltransferase domain; Region: Methyltransf_11; pfam08241 159087005498 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 159087005499 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005500 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 159087005501 active site 159087005502 phosphorylation site [posttranslational modification] 159087005503 intermolecular recognition site; other site 159087005504 dimerization interface [polypeptide binding]; other site 159087005505 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005506 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 159087005507 active site 159087005508 phosphorylation site [posttranslational modification] 159087005509 intermolecular recognition site; other site 159087005510 dimerization interface [polypeptide binding]; other site 159087005511 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087005512 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005513 metal binding site [ion binding]; metal-binding site 159087005514 active site 159087005515 I-site; other site 159087005516 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 159087005517 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 159087005518 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 159087005519 RmuC family; Region: RmuC; pfam02646 159087005520 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 159087005521 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087005522 Catalytic domain of Protein Kinases; Region: PKc; cd00180 159087005523 active site 159087005524 ATP binding site [chemical binding]; other site 159087005525 substrate binding site [chemical binding]; other site 159087005526 activation loop (A-loop); other site 159087005527 HDOD domain; Region: HDOD; pfam08668 159087005528 GAF domain; Region: GAF; pfam01590 159087005529 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 159087005530 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 159087005531 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 159087005532 RNA binding surface [nucleotide binding]; other site 159087005533 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 159087005534 active site 159087005535 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 159087005536 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 159087005537 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 159087005538 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 159087005539 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 159087005540 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 159087005541 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 159087005542 NAD(P) binding site [chemical binding]; other site 159087005543 homotetramer interface [polypeptide binding]; other site 159087005544 homodimer interface [polypeptide binding]; other site 159087005545 active site 159087005546 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 159087005547 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 159087005548 NAD(P) binding site [chemical binding]; other site 159087005549 homotetramer interface [polypeptide binding]; other site 159087005550 homodimer interface [polypeptide binding]; other site 159087005551 active site 159087005552 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 159087005553 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 159087005554 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 159087005555 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 159087005556 PAS fold; Region: PAS_4; pfam08448 159087005557 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 159087005558 putative active site [active] 159087005559 heme pocket [chemical binding]; other site 159087005560 PAS fold; Region: PAS_3; pfam08447 159087005561 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 159087005562 dimer interface [polypeptide binding]; other site 159087005563 phosphorylation site [posttranslational modification] 159087005564 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 159087005565 ATP binding site [chemical binding]; other site 159087005566 Mg2+ binding site [ion binding]; other site 159087005567 G-X-G motif; other site 159087005568 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005569 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 159087005570 active site 159087005571 phosphorylation site [posttranslational modification] 159087005572 intermolecular recognition site; other site 159087005573 dimerization interface [polypeptide binding]; other site 159087005574 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 159087005575 O-succinylbenzoate synthase; Provisional; Region: PRK05105 159087005576 active site 159087005577 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 159087005578 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 159087005579 substrate binding site [chemical binding]; other site 159087005580 oxyanion hole (OAH) forming residues; other site 159087005581 trimer interface [polypeptide binding]; other site 159087005582 Hemerythrin; Region: Hemerythrin; cd12107 159087005583 Fe binding site [ion binding]; other site 159087005584 PilZ domain; Region: PilZ; pfam07238 159087005585 Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]; Region: IlvH; COG0440 159087005586 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 159087005587 putative valine binding site [chemical binding]; other site 159087005588 dimer interface [polypeptide binding]; other site 159087005589 acetolactate synthase catalytic subunit; Validated; Region: PRK08155 159087005590 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 159087005591 PYR/PP interface [polypeptide binding]; other site 159087005592 dimer interface [polypeptide binding]; other site 159087005593 TPP binding site [chemical binding]; other site 159087005594 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 159087005595 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 159087005596 TPP-binding site [chemical binding]; other site 159087005597 dimer interface [polypeptide binding]; other site 159087005598 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 159087005599 PAS fold; Region: PAS_3; pfam08447 159087005600 putative active site [active] 159087005601 heme pocket [chemical binding]; other site 159087005602 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087005603 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 159087005604 dimer interface [polypeptide binding]; other site 159087005605 phosphorylation site [posttranslational modification] 159087005606 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 159087005607 ATP binding site [chemical binding]; other site 159087005608 Mg2+ binding site [ion binding]; other site 159087005609 G-X-G motif; other site 159087005610 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005611 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 159087005612 active site 159087005613 phosphorylation site [posttranslational modification] 159087005614 intermolecular recognition site; other site 159087005615 dimerization interface [polypeptide binding]; other site 159087005616 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087005617 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005618 metal binding site [ion binding]; metal-binding site 159087005619 active site 159087005620 I-site; other site 159087005621 metal ion transporter CorA-like divalent cation transporter superfamily; Region: MIT_CorA-like; cl00459 159087005622 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 159087005623 Fumarase C-terminus; Region: Fumerase_C; pfam05683 159087005624 hypothetical protein; Provisional; Region: PRK05208 159087005625 acetyl-CoA synthetase; Provisional; Region: PRK00174 159087005626 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 159087005627 active site 159087005628 CoA binding site [chemical binding]; other site 159087005629 acyl-activating enzyme (AAE) consensus motif; other site 159087005630 AMP binding site [chemical binding]; other site 159087005631 acetate binding site [chemical binding]; other site 159087005632 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 159087005633 Na binding site [ion binding]; other site 159087005634 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 159087005635 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087005636 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 159087005637 dimer interface [polypeptide binding]; other site 159087005638 phosphorylation site [posttranslational modification] 159087005639 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 159087005640 ATP binding site [chemical binding]; other site 159087005641 Mg2+ binding site [ion binding]; other site 159087005642 G-X-G motif; other site 159087005643 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005644 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 159087005645 active site 159087005646 phosphorylation site [posttranslational modification] 159087005647 intermolecular recognition site; other site 159087005648 dimerization interface [polypeptide binding]; other site 159087005649 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 159087005650 active site 159087005651 catalytic site [active] 159087005652 substrate binding site [chemical binding]; other site 159087005653 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087005654 metal binding triad; other site 159087005655 Putative nucleotidyltransferase substrate binding domain; Region: DUF294_C; pfam10335 159087005656 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 159087005657 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 159087005658 ligand binding site [chemical binding]; other site 159087005659 flexible hinge region; other site 159087005660 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 159087005661 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087005662 metal binding triad; other site 159087005663 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 159087005664 catalytic site [active] 159087005665 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 159087005666 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 159087005667 Na binding site [ion binding]; other site 159087005668 putative solute:sodium symporter small subunit; Region: Na_symport_sm; TIGR03647 159087005669 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 159087005670 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 159087005671 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087005672 The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; Region: PBP2_LysR_opines_like; cd08415 159087005673 putative dimerization interface [polypeptide binding]; other site 159087005674 diaminopimelate decarboxylase; Provisional; Region: PRK11165 159087005675 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 159087005676 active site 159087005677 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087005678 substrate binding site [chemical binding]; other site 159087005679 catalytic residues [active] 159087005680 dimer interface [polypeptide binding]; other site 159087005681 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 159087005682 IHF - DNA interface [nucleotide binding]; other site 159087005683 IHF dimer interface [polypeptide binding]; other site 159087005684 bifunctional HTH-domain containing protein/aminotransferase; Provisional; Region: PRK13355 159087005685 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 159087005686 putative transposase OrfB; Reviewed; Region: PHA02517 159087005687 HTH-like domain; Region: HTH_21; pfam13276 159087005688 Integrase core domain; Region: rve; pfam00665 159087005689 Integrase core domain; Region: rve_3; pfam13683 159087005690 phage/plasmid-like protein TIGR03299; Region: LGT_TIGR03299 159087005691 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 159087005692 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 159087005693 IHF dimer interface [polypeptide binding]; other site 159087005694 IHF - DNA interface [nucleotide binding]; other site 159087005695 Hemerythrin; Region: Hemerythrin; cd12107 159087005696 Fe binding site [ion binding]; other site 159087005697 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005698 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 159087005699 active site 159087005700 phosphorylation site [posttranslational modification] 159087005701 intermolecular recognition site; other site 159087005702 dimerization interface [polypeptide binding]; other site 159087005703 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005704 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 159087005705 active site 159087005706 phosphorylation site [posttranslational modification] 159087005707 intermolecular recognition site; other site 159087005708 dimerization interface [polypeptide binding]; other site 159087005709 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 159087005710 PAS fold; Region: PAS_3; pfam08447 159087005711 putative active site [active] 159087005712 heme pocket [chemical binding]; other site 159087005713 PAS domain S-box; Region: sensory_box; TIGR00229 159087005714 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 159087005715 putative active site [active] 159087005716 heme pocket [chemical binding]; other site 159087005717 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087005718 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005719 metal binding site [ion binding]; metal-binding site 159087005720 active site 159087005721 I-site; other site 159087005722 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005723 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 159087005724 active site 159087005725 phosphorylation site [posttranslational modification] 159087005726 intermolecular recognition site; other site 159087005727 dimerization interface [polypeptide binding]; other site 159087005728 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087005729 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005730 metal binding site [ion binding]; metal-binding site 159087005731 active site 159087005732 I-site; other site 159087005733 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087005734 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 159087005735 dimer interface [polypeptide binding]; other site 159087005736 phosphorylation site [posttranslational modification] 159087005737 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 159087005738 ATP binding site [chemical binding]; other site 159087005739 Mg2+ binding site [ion binding]; other site 159087005740 G-X-G motif; other site 159087005741 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087005742 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 159087005743 ligand binding site [chemical binding]; other site 159087005744 flexible hinge region; other site 159087005745 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 159087005746 Hemerythrin; Region: Hemerythrin; cd12107 159087005747 Fe binding site [ion binding]; other site 159087005748 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087005749 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 159087005750 Walker A/P-loop; other site 159087005751 ATP binding site [chemical binding]; other site 159087005752 Q-loop/lid; other site 159087005753 ABC transporter signature motif; other site 159087005754 Walker B; other site 159087005755 D-loop; other site 159087005756 H-loop/switch region; other site 159087005757 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087005758 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087005759 FtsX-like permease family; Region: FtsX; pfam02687 159087005760 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087005761 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087005762 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087005763 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087005764 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087005765 integrase; Provisional; Region: PRK09692 159087005766 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 159087005767 active site 159087005768 Int/Topo IB signature motif; other site 159087005769 Cache domain; Region: Cache_1; pfam02743 159087005770 PAS fold; Region: PAS_4; pfam08448 159087005771 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 159087005772 putative active site [active] 159087005773 heme pocket [chemical binding]; other site 159087005774 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 159087005775 PAS domain; Region: PAS_9; pfam13426 159087005776 putative active site [active] 159087005777 heme pocket [chemical binding]; other site 159087005778 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087005779 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087005780 metal binding site [ion binding]; metal-binding site 159087005781 active site 159087005782 I-site; other site 159087005783 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 159087005784 H+ Antiporter protein; Region: 2A0121; TIGR00900 159087005785 Domain of unknown function (DUF336); Region: DUF336; pfam03928 159087005786 acetylornithine transaminase protein; Provisional; Region: argD; PRK03715 159087005787 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 159087005788 inhibitor-cofactor binding pocket; inhibition site 159087005789 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087005790 catalytic residue [active] 159087005791 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 159087005792 Response regulator receiver domain; Region: Response_reg; pfam00072 159087005793 active site 159087005794 phosphorylation site [posttranslational modification] 159087005795 intermolecular recognition site; other site 159087005796 dimerization interface [polypeptide binding]; other site 159087005797 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 159087005798 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 159087005799 active site 159087005800 dimerization interface [polypeptide binding]; other site 159087005801 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 159087005802 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 159087005803 HDOD domain; Region: HDOD; pfam08668 159087005804 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087005805 Zn2+ binding site [ion binding]; other site 159087005806 Mg2+ binding site [ion binding]; other site 159087005807 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087005808 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 159087005809 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 159087005810 active site 159087005811 SAM binding site [chemical binding]; other site 159087005812 homodimer interface [polypeptide binding]; other site 159087005813 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 159087005814 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 159087005815 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 159087005816 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 159087005817 active site 159087005818 SAM binding site [chemical binding]; other site 159087005819 homodimer interface [polypeptide binding]; other site 159087005820 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 159087005821 active site 159087005822 putative homodimer interface [polypeptide binding]; other site 159087005823 SAM binding site [chemical binding]; other site 159087005824 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 159087005825 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 159087005826 S-adenosylmethionine binding site [chemical binding]; other site 159087005827 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 159087005828 Precorrin-8X methylmutase; Region: CbiC; pfam02570 159087005829 cobalt-precorrin-8X methylmutase; Validated; Region: cbiC; cl00913 159087005830 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 159087005831 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 159087005832 putative active site [active] 159087005833 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_C; cd03414 159087005834 putative active site [active] 159087005835 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 159087005836 active site 159087005837 SAM binding site [chemical binding]; other site 159087005838 homodimer interface [polypeptide binding]; other site 159087005839 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 159087005840 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 159087005841 Walker A/P-loop; other site 159087005842 ATP binding site [chemical binding]; other site 159087005843 Q-loop/lid; other site 159087005844 ABC transporter signature motif; other site 159087005845 Walker B; other site 159087005846 D-loop; other site 159087005847 H-loop/switch region; other site 159087005848 Cobalt transport protein; Region: CbiQ; cl00463 159087005849 cobalt transport protein CbiN; Provisional; Region: PRK02898 159087005850 cobalt transport protein CbiM; Validated; Region: PRK08319 159087005851 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 159087005852 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 159087005853 TAP-like protein; Region: Abhydrolase_4; pfam08386 159087005854 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 159087005855 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 159087005856 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 159087005857 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 159087005858 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 159087005859 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 159087005860 FeS/SAM binding site; other site 159087005861 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 159087005862 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 159087005863 GtrA-like protein; Region: GtrA; pfam04138 159087005864 hypothetical protein; Provisional; Region: PRK07233 159087005865 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 159087005866 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 159087005867 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087005868 NAD(P) binding site [chemical binding]; other site 159087005869 active site 159087005870 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 159087005871 classical (c) SDRs; Region: SDR_c; cd05233 159087005872 NAD(P) binding site [chemical binding]; other site 159087005873 active site 159087005874 FAD binding domain; Region: FAD_binding_4; pfam01565 159087005875 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087005876 hypothetical protein; Validated; Region: PRK08238 159087005877 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 159087005878 phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional; Region: PRK12324 159087005879 putative transposase OrfB; Reviewed; Region: PHA02517 159087005880 HTH-like domain; Region: HTH_21; pfam13276 159087005881 Integrase core domain; Region: rve; pfam00665 159087005882 Integrase core domain; Region: rve_3; pfam13683 159087005883 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 159087005884 IHF dimer interface [polypeptide binding]; other site 159087005885 IHF - DNA interface [nucleotide binding]; other site 159087005886 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 159087005887 Found in ATP-dependent protease La (LON); Region: LON; smart00464 159087005888 Found in ATP-dependent protease La (LON); Region: LON; smart00464 159087005889 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 159087005890 Walker A motif; other site 159087005891 ATP binding site [chemical binding]; other site 159087005892 Walker B motif; other site 159087005893 arginine finger; other site 159087005894 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 159087005895 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 159087005896 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 159087005897 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 159087005898 Walker A motif; other site 159087005899 ATP binding site [chemical binding]; other site 159087005900 Walker B motif; other site 159087005901 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 159087005902 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 159087005903 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 159087005904 oligomer interface [polypeptide binding]; other site 159087005905 active site residues [active] 159087005906 trigger factor; Provisional; Region: tig; PRK01490 159087005907 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 159087005908 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 159087005909 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 159087005910 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 159087005911 metal binding site [ion binding]; metal-binding site 159087005912 dimer interface [polypeptide binding]; other site 159087005913 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 159087005914 HemK family putative methylases; Region: hemK_fam; TIGR00536 159087005915 capsule biosynthesis phosphatase; Region: EcbF-BcbF; TIGR01689 159087005916 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 159087005917 S-adenosylmethionine binding site [chemical binding]; other site 159087005918 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 159087005919 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 159087005920 metal binding site [ion binding]; metal-binding site 159087005921 dimer interface [polypeptide binding]; other site 159087005922 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 159087005923 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 159087005924 Walker A motif; other site 159087005925 ATP binding site [chemical binding]; other site 159087005926 Walker B motif; other site 159087005927 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 159087005928 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 159087005929 trimer interface [polypeptide binding]; other site 159087005930 active site 159087005931 substrate binding site [chemical binding]; other site 159087005932 CoA binding site [chemical binding]; other site 159087005933 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 159087005934 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 159087005935 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087005936 homodimer interface [polypeptide binding]; other site 159087005937 catalytic residue [active] 159087005938 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 159087005939 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087005940 Zn2+ binding site [ion binding]; other site 159087005941 Mg2+ binding site [ion binding]; other site 159087005942 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 159087005943 nucleoside/Zn binding site; other site 159087005944 dimer interface [polypeptide binding]; other site 159087005945 catalytic motif [active] 159087005946 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 159087005947 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 159087005948 Walker A/P-loop; other site 159087005949 ATP binding site [chemical binding]; other site 159087005950 Q-loop/lid; other site 159087005951 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 159087005952 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 159087005953 ABC transporter signature motif; other site 159087005954 Walker B; other site 159087005955 D-loop; other site 159087005956 H-loop/switch region; other site 159087005957 ZipA, C-terminal domain (FtsZ-binding); Region: ZipA_C; smart00771 159087005958 FtsZ protein binding site [polypeptide binding]; other site 159087005959 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 159087005960 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 159087005961 nucleotide binding pocket [chemical binding]; other site 159087005962 K-X-D-G motif; other site 159087005963 catalytic site [active] 159087005964 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 159087005965 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 159087005966 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 159087005967 Dimer interface [polypeptide binding]; other site 159087005968 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 159087005969 active site 159087005970 tetramer interface; other site 159087005971 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 159087005972 active site 159087005973 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 159087005974 S-adenosylmethionine binding site [chemical binding]; other site 159087005975 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 159087005976 PII uridylyl-transferase; Provisional; Region: PRK03059 159087005977 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087005978 metal binding triad; other site 159087005979 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 159087005980 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087005981 Zn2+ binding site [ion binding]; other site 159087005982 Mg2+ binding site [ion binding]; other site 159087005983 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 159087005984 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 159087005985 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 159087005986 active site 159087005987 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 159087005988 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 159087005989 NADP binding site [chemical binding]; other site 159087005990 active site 159087005991 putative substrate binding site [chemical binding]; other site 159087005992 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 159087005993 rRNA interaction site [nucleotide binding]; other site 159087005994 S8 interaction site; other site 159087005995 putative laminin-1 binding site; other site 159087005996 elongation factor Ts; Provisional; Region: tsf; PRK09377 159087005997 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 159087005998 Elongation factor TS; Region: EF_TS; pfam00889 159087005999 Elongation factor TS; Region: EF_TS; pfam00889 159087006000 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 159087006001 putative nucleotide binding site [chemical binding]; other site 159087006002 uridine monophosphate binding site [chemical binding]; other site 159087006003 homohexameric interface [polypeptide binding]; other site 159087006004 ribosome recycling factor; Reviewed; Region: frr; PRK00083 159087006005 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 159087006006 hinge region; other site 159087006007 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 159087006008 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 159087006009 catalytic residue [active] 159087006010 putative FPP diphosphate binding site; other site 159087006011 putative FPP binding hydrophobic cleft; other site 159087006012 dimer interface [polypeptide binding]; other site 159087006013 putative IPP diphosphate binding site; other site 159087006014 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 159087006015 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 159087006016 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 159087006017 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 159087006018 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 159087006019 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 159087006020 zinc metallopeptidase RseP; Provisional; Region: PRK10779 159087006021 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 159087006022 active site 159087006023 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 159087006024 protein binding site [polypeptide binding]; other site 159087006025 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 159087006026 protein binding site [polypeptide binding]; other site 159087006027 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 159087006028 putative substrate binding region [chemical binding]; other site 159087006029 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 159087006030 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 159087006031 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 159087006032 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 159087006033 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 159087006034 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 159087006035 Surface antigen; Region: Bac_surface_Ag; pfam01103 159087006036 periplasmic chaperone; Provisional; Region: PRK10780 159087006037 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 159087006038 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 159087006039 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 159087006040 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 159087006041 trimer interface [polypeptide binding]; other site 159087006042 active site 159087006043 UDP-GlcNAc binding site [chemical binding]; other site 159087006044 lipid binding site [chemical binding]; lipid-binding site 159087006045 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 159087006046 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 159087006047 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 159087006048 active site 159087006049 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 159087006050 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 159087006051 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 159087006052 RNA/DNA hybrid binding site [nucleotide binding]; other site 159087006053 active site 159087006054 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 159087006055 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 159087006056 PEP synthetase regulatory protein; Provisional; Region: PRK05339 159087006057 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 159087006058 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 159087006059 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 159087006060 Ligand Binding Site [chemical binding]; other site 159087006061 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 159087006062 Ligand Binding Site [chemical binding]; other site 159087006063 L-lactate permease; Region: Lactate_perm; cl00701 159087006064 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 159087006065 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087006066 FAD binding domain; Region: FAD_binding_4; pfam01565 159087006067 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 159087006068 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 159087006069 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 159087006070 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 159087006071 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 159087006072 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 159087006073 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 159087006074 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 159087006075 Cysteine-rich domain; Region: CCG; pfam02754 159087006076 Cysteine-rich domain; Region: CCG; pfam02754 159087006077 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 159087006078 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087006079 DNA-binding site [nucleotide binding]; DNA binding site 159087006080 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 159087006081 phosphoenolpyruvate synthase; Validated; Region: PRK06464 159087006082 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 159087006083 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 159087006084 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 159087006085 Cache domain; Region: Cache_2; cl07034 159087006086 Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only]; Region: COG3240 159087006087 Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: fatty_acyltransferase_like; cd01846 159087006088 active site 159087006089 catalytic triad [active] 159087006090 oxyanion hole [active] 159087006091 PEP-CTERM motif; Region: VPEP; pfam07589 159087006092 Response regulator receiver domain; Region: Response_reg; pfam00072 159087006093 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 159087006094 active site 159087006095 phosphorylation site [posttranslational modification] 159087006096 intermolecular recognition site; other site 159087006097 dimerization interface [polypeptide binding]; other site 159087006098 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 159087006099 PAS fold; Region: PAS_3; pfam08447 159087006100 putative active site [active] 159087006101 heme pocket [chemical binding]; other site 159087006102 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087006103 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006104 metal binding site [ion binding]; metal-binding site 159087006105 active site 159087006106 I-site; other site 159087006107 PAS fold; Region: PAS_4; pfam08448 159087006108 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 159087006109 PAS domain; Region: PAS_9; pfam13426 159087006110 putative active site [active] 159087006111 heme pocket [chemical binding]; other site 159087006112 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 159087006113 putative active site [active] 159087006114 PAS fold; Region: PAS_3; pfam08447 159087006115 heme pocket [chemical binding]; other site 159087006116 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087006117 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 159087006118 dimer interface [polypeptide binding]; other site 159087006119 phosphorylation site [posttranslational modification] 159087006120 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 159087006121 ATP binding site [chemical binding]; other site 159087006122 Mg2+ binding site [ion binding]; other site 159087006123 G-X-G motif; other site 159087006124 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087006125 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 159087006126 active site 159087006127 phosphorylation site [posttranslational modification] 159087006128 intermolecular recognition site; other site 159087006129 dimerization interface [polypeptide binding]; other site 159087006130 2'-5' RNA ligase superfamily; Region: 2_5_RNA_ligase2; pfam13563 159087006131 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 159087006132 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 159087006133 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 159087006134 catalytic loop [active] 159087006135 iron binding site [ion binding]; other site 159087006136 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 159087006137 L-aspartate oxidase; Provisional; Region: PRK06175 159087006138 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 159087006139 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 159087006140 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 159087006141 Iron-sulfur protein interface; other site 159087006142 proximal heme binding site [chemical binding]; other site 159087006143 distal heme binding site [chemical binding]; other site 159087006144 dimer interface [polypeptide binding]; other site 159087006145 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 159087006146 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 159087006147 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 159087006148 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 159087006149 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 159087006150 Walker A motif; other site 159087006151 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 159087006152 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 159087006153 dimer interface [polypeptide binding]; other site 159087006154 putative functional site; other site 159087006155 putative MPT binding site; other site 159087006156 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 159087006157 MoaE interaction surface [polypeptide binding]; other site 159087006158 MoeB interaction surface [polypeptide binding]; other site 159087006159 thiocarboxylated glycine; other site 159087006160 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 159087006161 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 159087006162 GTP/Mg2+ binding site [chemical binding]; other site 159087006163 G4 box; other site 159087006164 G5 box; other site 159087006165 G1 box; other site 159087006166 Switch I region; other site 159087006167 G2 box; other site 159087006168 G3 box; other site 159087006169 Switch II region; other site 159087006170 HDOD domain; Region: HDOD; pfam08668 159087006171 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 159087006172 Zn2+ binding site [ion binding]; other site 159087006173 Mg2+ binding site [ion binding]; other site 159087006174 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 159087006175 active site residue [active] 159087006176 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 159087006177 YaeQ protein; Region: YaeQ; pfam07152 159087006178 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087006179 ligand binding site [chemical binding]; other site 159087006180 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 159087006181 FOG: CBS domain [General function prediction only]; Region: COG0517 159087006182 Transcription factor zinc-finger; Region: zf-TFIIB; pfam13453 159087006183 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 159087006184 Peptidase family U32; Region: Peptidase_U32; pfam01136 159087006185 Collagenase; Region: DUF3656; pfam12392 159087006186 Methyltransferase domain; Region: Methyltransf_32; pfam13679 159087006187 Methyltransferase domain; Region: Methyltransf_31; pfam13847 159087006188 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 159087006189 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087006190 Walker A/P-loop; other site 159087006191 ATP binding site [chemical binding]; other site 159087006192 Q-loop/lid; other site 159087006193 ABC transporter signature motif; other site 159087006194 Walker B; other site 159087006195 D-loop; other site 159087006196 H-loop/switch region; other site 159087006197 ABC transporter; Region: ABC_tran_2; pfam12848 159087006198 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087006199 hypothetical protein; Provisional; Region: PRK14852 159087006200 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 159087006201 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087006202 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 159087006203 dimer interface [polypeptide binding]; other site 159087006204 phosphorylation site [posttranslational modification] 159087006205 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 159087006206 ATP binding site [chemical binding]; other site 159087006207 Mg2+ binding site [ion binding]; other site 159087006208 G-X-G motif; other site 159087006209 response regulator GlrR; Provisional; Region: PRK15115 159087006210 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 159087006211 active site 159087006212 phosphorylation site [posttranslational modification] 159087006213 intermolecular recognition site; other site 159087006214 dimerization interface [polypeptide binding]; other site 159087006215 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 159087006216 Walker A motif; other site 159087006217 ATP binding site [chemical binding]; other site 159087006218 Walker B motif; other site 159087006219 arginine finger; other site 159087006220 BON domain; Region: BON; pfam04972 159087006221 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087006222 DsrE/DsrF/DrsH-like family; Region: DrsE_2; cl17453 159087006223 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 159087006224 lipoyl attachment site [posttranslational modification]; other site 159087006225 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 159087006226 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 159087006227 G1 box; other site 159087006228 putative GEF interaction site [polypeptide binding]; other site 159087006229 GTP/Mg2+ binding site [chemical binding]; other site 159087006230 Switch I region; other site 159087006231 G2 box; other site 159087006232 G3 box; other site 159087006233 Switch II region; other site 159087006234 G4 box; other site 159087006235 G5 box; other site 159087006236 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 159087006237 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 159087006238 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 159087006239 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 159087006240 MOSC domain; Region: MOSC; pfam03473 159087006241 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 159087006242 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 159087006243 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 159087006244 selenocysteine synthase; Provisional; Region: PRK04311 159087006245 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 159087006246 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 159087006247 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087006248 catalytic residue [active] 159087006249 Protein involved in formate dehydrogenase formation; Region: FdhE; pfam04216 159087006250 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 159087006251 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 159087006252 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 159087006253 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 159087006254 4Fe-4S binding domain; Region: Fer4; cl02805 159087006255 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 159087006256 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 159087006257 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 159087006258 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 159087006259 molybdopterin cofactor binding site; other site 159087006260 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 159087006261 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 159087006262 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087006263 ATP binding site [chemical binding]; other site 159087006264 Mg++ binding site [ion binding]; other site 159087006265 motif III; other site 159087006266 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 159087006267 nucleotide binding region [chemical binding]; other site 159087006268 ATP-binding site [chemical binding]; other site 159087006269 DsrE/DsrF-like family; Region: DrsE; cl00672 159087006270 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 159087006271 dimer interface [polypeptide binding]; other site 159087006272 phosphorylation site [posttranslational modification] 159087006273 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 159087006274 ATP binding site [chemical binding]; other site 159087006275 Mg2+ binding site [ion binding]; other site 159087006276 G-X-G motif; other site 159087006277 Response regulator receiver domain; Region: Response_reg; pfam00072 159087006278 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 159087006279 active site 159087006280 phosphorylation site [posttranslational modification] 159087006281 intermolecular recognition site; other site 159087006282 dimerization interface [polypeptide binding]; other site 159087006283 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 159087006284 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 159087006285 S-adenosylmethionine binding site [chemical binding]; other site 159087006286 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 159087006287 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 159087006288 dimer interface [polypeptide binding]; other site 159087006289 conserved gate region; other site 159087006290 putative PBP binding loops; other site 159087006291 ABC-ATPase subunit interface; other site 159087006292 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 159087006293 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 159087006294 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 159087006295 Walker A/P-loop; other site 159087006296 ATP binding site [chemical binding]; other site 159087006297 Q-loop/lid; other site 159087006298 ABC transporter signature motif; other site 159087006299 Walker B; other site 159087006300 D-loop; other site 159087006301 H-loop/switch region; other site 159087006302 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087006303 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 159087006304 substrate binding pocket [chemical binding]; other site 159087006305 membrane-bound complex binding site; other site 159087006306 hinge residues; other site 159087006307 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087006308 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 159087006309 active site 159087006310 phosphorylation site [posttranslational modification] 159087006311 intermolecular recognition site; other site 159087006312 dimerization interface [polypeptide binding]; other site 159087006313 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 159087006314 Walker A motif; other site 159087006315 ATP binding site [chemical binding]; other site 159087006316 Walker B motif; other site 159087006317 arginine finger; other site 159087006318 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087006319 HAMP domain; Region: HAMP; pfam00672 159087006320 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 159087006321 dimer interface [polypeptide binding]; other site 159087006322 phosphorylation site [posttranslational modification] 159087006323 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 159087006324 ATP binding site [chemical binding]; other site 159087006325 Mg2+ binding site [ion binding]; other site 159087006326 G-X-G motif; other site 159087006327 NosL; Region: NosL; pfam05573 159087006328 Family description; Region: DsbD_2; pfam13386 159087006329 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 159087006330 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087006331 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 159087006332 DNA binding residues [nucleotide binding] 159087006333 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 159087006334 FecR protein; Region: FecR; pfam04773 159087006335 Secretin and TonB N terminus short domain; Region: STN; smart00965 159087006336 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 159087006337 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 159087006338 N-terminal plug; other site 159087006339 ligand-binding site [chemical binding]; other site 159087006340 NosL; Region: NosL; cl01769 159087006341 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087006342 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 159087006343 metal-binding site [ion binding] 159087006344 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087006345 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 159087006346 motif II; other site 159087006347 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 159087006348 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 159087006349 catalytic residues [active] 159087006350 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087006351 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 159087006352 Walker A/P-loop; other site 159087006353 ATP binding site [chemical binding]; other site 159087006354 Q-loop/lid; other site 159087006355 ABC transporter signature motif; other site 159087006356 Walker B; other site 159087006357 D-loop; other site 159087006358 H-loop/switch region; other site 159087006359 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 159087006360 FtsX-like permease family; Region: FtsX; pfam02687 159087006361 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 159087006362 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 159087006363 Cu(I) binding site [ion binding]; other site 159087006364 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 159087006365 NAD-dependent deacetylase; Provisional; Region: PRK00481 159087006366 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 159087006367 NAD+ binding site [chemical binding]; other site 159087006368 substrate binding site [chemical binding]; other site 159087006369 Zn binding site [ion binding]; other site 159087006370 Phasin protein; Region: Phasin_2; pfam09361 159087006371 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 159087006372 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 159087006373 CAP-like domain; other site 159087006374 active site 159087006375 primary dimer interface [polypeptide binding]; other site 159087006376 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 159087006377 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 159087006378 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087006379 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 159087006380 Soluble P-type ATPase [General function prediction only]; Region: COG4087 159087006381 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 159087006382 Domain of unknown function (DUF3597); Region: DUF3597; pfam12200 159087006383 Leucine rich repeat; Region: LRR_8; pfam13855 159087006384 Leucine rich repeat; Region: LRR_8; pfam13855 159087006385 Protein tyrosine kinase; Region: Pkinase_Tyr; pfam07714 159087006386 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 159087006387 active site 159087006388 ATP binding site [chemical binding]; other site 159087006389 substrate binding site [chemical binding]; other site 159087006390 activation loop (A-loop); other site 159087006391 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 159087006392 B12 binding site [chemical binding]; other site 159087006393 Radical SAM superfamily; Region: Radical_SAM; pfam04055 159087006394 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 159087006395 S-adenosylmethionine binding site [chemical binding]; other site 159087006396 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 159087006397 Coenzyme A binding pocket [chemical binding]; other site 159087006398 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 159087006399 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 159087006400 active site 159087006401 nucleophile elbow; other site 159087006402 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 159087006403 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087006404 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087006405 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 159087006406 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087006407 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 159087006408 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 159087006409 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 159087006410 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 159087006411 nucleophile elbow; other site 159087006412 Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning]; Region: RIO1; COG1718 159087006413 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 159087006414 ATP binding site [chemical binding]; other site 159087006415 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 159087006416 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 159087006417 ATP binding site [chemical binding]; other site 159087006418 Mg2+ binding site [ion binding]; other site 159087006419 G-X-G motif; other site 159087006420 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 159087006421 anchoring element; other site 159087006422 dimer interface [polypeptide binding]; other site 159087006423 ATP binding site [chemical binding]; other site 159087006424 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 159087006425 active site 159087006426 putative metal-binding site [ion binding]; other site 159087006427 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 159087006428 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 159087006429 dimer interface [polypeptide binding]; other site 159087006430 FMN binding site [chemical binding]; other site 159087006431 Protein of unknown function (DUF808); Region: DUF808; pfam05661 159087006432 Double zinc ribbon; Region: DZR; pfam12773 159087006433 Acyltransferase family; Region: Acyl_transf_3; pfam01757 159087006434 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 159087006435 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 159087006436 hypothetical protein; Reviewed; Region: PRK09588 159087006437 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 159087006438 hydrophobic ligand binding site; other site 159087006439 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087006440 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087006441 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087006442 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087006443 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087006444 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087006445 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 159087006446 active site 159087006447 phosphorylation site [posttranslational modification] 159087006448 intermolecular recognition site; other site 159087006449 dimerization interface [polypeptide binding]; other site 159087006450 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 159087006451 DNA binding site [nucleotide binding] 159087006452 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 159087006453 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087006454 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 159087006455 dimer interface [polypeptide binding]; other site 159087006456 phosphorylation site [posttranslational modification] 159087006457 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 159087006458 ATP binding site [chemical binding]; other site 159087006459 Mg2+ binding site [ion binding]; other site 159087006460 G-X-G motif; other site 159087006461 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 159087006462 hypothetical protein; Provisional; Region: PRK11295 159087006463 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 159087006464 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 159087006465 active site 159087006466 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 159087006467 Radical SAM superfamily; Region: Radical_SAM; pfam04055 159087006468 FeS/SAM binding site; other site 159087006469 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 159087006470 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087006471 putative substrate translocation pore; other site 159087006472 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 159087006473 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 159087006474 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087006475 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 159087006476 AAA domain; Region: AAA_21; pfam13304 159087006477 methionine sulfoxide reductase B; Provisional; Region: PRK00222 159087006478 SelR domain; Region: SelR; pfam01641 159087006479 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 159087006480 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 159087006481 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087006482 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 159087006483 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 159087006484 catalytic loop [active] 159087006485 iron binding site [ion binding]; other site 159087006486 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 159087006487 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 159087006488 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 159087006489 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 159087006490 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 159087006491 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 159087006492 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 159087006493 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 159087006494 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 159087006495 XdhC Rossmann domain; Region: XdhC_C; pfam13478 159087006496 NAD binding site [chemical binding]; other site 159087006497 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 159087006498 Ligand binding site; other site 159087006499 metal-binding site 159087006500 Uncharacterized protein family (UPF0149); Region: UPF0149; pfam03695 159087006501 SEC-C motif; Region: SEC-C; pfam02810 159087006502 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 159087006503 PAS fold; Region: PAS_4; pfam08448 159087006504 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 159087006505 putative active site [active] 159087006506 heme pocket [chemical binding]; other site 159087006507 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 159087006508 PAS fold; Region: PAS_3; pfam08447 159087006509 putative active site [active] 159087006510 heme pocket [chemical binding]; other site 159087006511 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087006512 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 159087006513 dimer interface [polypeptide binding]; other site 159087006514 phosphorylation site [posttranslational modification] 159087006515 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 159087006516 ATP binding site [chemical binding]; other site 159087006517 Mg2+ binding site [ion binding]; other site 159087006518 G-X-G motif; other site 159087006519 Response regulator receiver domain; Region: Response_reg; pfam00072 159087006520 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 159087006521 active site 159087006522 phosphorylation site [posttranslational modification] 159087006523 intermolecular recognition site; other site 159087006524 dimerization interface [polypeptide binding]; other site 159087006525 CHASE2 domain; Region: CHASE2; pfam05226 159087006526 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087006527 Zn2+ binding site [ion binding]; other site 159087006528 Mg2+ binding site [ion binding]; other site 159087006529 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087006530 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087006531 ligand binding site [chemical binding]; other site 159087006532 FecR protein; Region: FecR; pfam04773 159087006533 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 159087006534 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 159087006535 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 159087006536 protein binding site [polypeptide binding]; other site 159087006537 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 159087006538 protein binding site [polypeptide binding]; other site 159087006539 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 159087006540 dimerization interface [polypeptide binding]; other site 159087006541 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087006542 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087006543 dimer interface [polypeptide binding]; other site 159087006544 putative CheW interface [polypeptide binding]; other site 159087006545 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]; Region: COG3613 159087006546 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 159087006547 CreA protein; Region: CreA; pfam05981 159087006548 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 159087006549 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 159087006550 active site 159087006551 nucleophile elbow; other site 159087006552 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 159087006553 active site 159087006554 catalytic site [active] 159087006555 substrate binding site [chemical binding]; other site 159087006556 nucleotide excision repair endonuclease; Provisional; Region: PRK10545 159087006557 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 159087006558 GIY-YIG motif/motif A; other site 159087006559 active site 159087006560 catalytic site [active] 159087006561 putative DNA binding site [nucleotide binding]; other site 159087006562 metal binding site [ion binding]; metal-binding site 159087006563 PAS fold; Region: PAS_4; pfam08448 159087006564 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 159087006565 putative active site [active] 159087006566 heme pocket [chemical binding]; other site 159087006567 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 159087006568 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087006569 putative active site [active] 159087006570 heme pocket [chemical binding]; other site 159087006571 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087006572 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006573 metal binding site [ion binding]; metal-binding site 159087006574 active site 159087006575 I-site; other site 159087006576 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 159087006577 Cupin; Region: Cupin_6; pfam12852 159087006578 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 159087006579 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087006580 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these...; Region: PRX_like2; cd02970 159087006581 putative catalytic residues [active] 159087006582 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 159087006583 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 159087006584 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 159087006585 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087006586 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; pfam10137 159087006587 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087006588 AAA domain; Region: AAA_23; pfam13476 159087006589 Walker A/P-loop; other site 159087006590 ATP binding site [chemical binding]; other site 159087006591 Q-loop/lid; other site 159087006592 exonuclease subunit SbcC; Provisional; Region: PRK10246 159087006593 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087006594 ABC transporter signature motif; other site 159087006595 Walker B; other site 159087006596 D-loop; other site 159087006597 H-loop/switch region; other site 159087006598 exonuclease subunit SbcD; Provisional; Region: PRK10966 159087006599 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 159087006600 active site 159087006601 metal binding site [ion binding]; metal-binding site 159087006602 DNA binding site [nucleotide binding] 159087006603 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 159087006604 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 159087006605 glycerol kinase; Provisional; Region: glpK; PRK00047 159087006606 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 159087006607 N- and C-terminal domain interface [polypeptide binding]; other site 159087006608 active site 159087006609 MgATP binding site [chemical binding]; other site 159087006610 catalytic site [active] 159087006611 metal binding site [ion binding]; metal-binding site 159087006612 glycerol binding site [chemical binding]; other site 159087006613 homotetramer interface [polypeptide binding]; other site 159087006614 homodimer interface [polypeptide binding]; other site 159087006615 FBP binding site [chemical binding]; other site 159087006616 protein IIAGlc interface [polypeptide binding]; other site 159087006617 Uncharacterized conserved protein (DUF2164); Region: DUF2164; pfam09932 159087006618 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 159087006619 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 159087006620 dimerization interface [polypeptide binding]; other site 159087006621 ATP binding site [chemical binding]; other site 159087006622 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 159087006623 dimerization interface [polypeptide binding]; other site 159087006624 ATP binding site [chemical binding]; other site 159087006625 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 159087006626 putative active site [active] 159087006627 catalytic triad [active] 159087006628 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 159087006629 oligomer interface [polypeptide binding]; other site 159087006630 active site residues [active] 159087006631 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 159087006632 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 159087006633 putative ADP-ribose binding site [chemical binding]; other site 159087006634 putative active site [active] 159087006635 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 159087006636 active site residue [active] 159087006637 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 159087006638 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 159087006639 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087006640 DNA-binding site [nucleotide binding]; DNA binding site 159087006641 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 159087006642 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087006643 homodimer interface [polypeptide binding]; other site 159087006644 catalytic residue [active] 159087006645 periplasmic folding chaperone; Provisional; Region: PRK10788 159087006646 SurA N-terminal domain; Region: SurA_N_3; cl07813 159087006647 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 159087006648 PAS domain S-box; Region: sensory_box; TIGR00229 159087006649 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 159087006650 putative active site [active] 159087006651 heme pocket [chemical binding]; other site 159087006652 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 159087006653 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 159087006654 putative active site [active] 159087006655 heme pocket [chemical binding]; other site 159087006656 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 159087006657 dimer interface [polypeptide binding]; other site 159087006658 phosphorylation site [posttranslational modification] 159087006659 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 159087006660 ATP binding site [chemical binding]; other site 159087006661 Mg2+ binding site [ion binding]; other site 159087006662 G-X-G motif; other site 159087006663 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087006664 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 159087006665 active site 159087006666 phosphorylation site [posttranslational modification] 159087006667 intermolecular recognition site; other site 159087006668 dimerization interface [polypeptide binding]; other site 159087006669 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 159087006670 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 159087006671 NAD binding site [chemical binding]; other site 159087006672 homotetramer interface [polypeptide binding]; other site 159087006673 homodimer interface [polypeptide binding]; other site 159087006674 substrate binding site [chemical binding]; other site 159087006675 active site 159087006676 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 159087006677 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 159087006678 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 159087006679 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 159087006680 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 159087006681 active site 159087006682 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 159087006683 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087006684 Zn2+ binding site [ion binding]; other site 159087006685 Mg2+ binding site [ion binding]; other site 159087006686 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 159087006687 LexA repressor; Validated; Region: PRK00215 159087006688 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 159087006689 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 159087006690 Catalytic site [active] 159087006691 Uncharacterized conserved protein [Function unknown]; Region: COG4544 159087006692 DNA Polymerase Y-family; Region: PolY_like; cd03468 159087006693 active site 159087006694 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 159087006695 DNA binding site [nucleotide binding] 159087006696 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 159087006697 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 159087006698 putative active site [active] 159087006699 putative PHP Thumb interface [polypeptide binding]; other site 159087006700 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 159087006701 generic binding surface II; other site 159087006702 generic binding surface I; other site 159087006703 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 159087006704 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 159087006705 binding surface 159087006706 TPR motif; other site 159087006707 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 159087006708 binding surface 159087006709 TPR motif; other site 159087006710 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 159087006711 TPR motif; other site 159087006712 binding surface 159087006713 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 159087006714 TPR motif; other site 159087006715 binding surface 159087006716 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 159087006717 TPR motif; other site 159087006718 binding surface 159087006719 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 159087006720 binding surface 159087006721 TPR motif; other site 159087006722 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087006723 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 159087006724 Beta-lactamase; Region: Beta-lactamase; pfam00144 159087006725 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 159087006726 serine O-acetyltransferase; Region: cysE; TIGR01172 159087006727 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 159087006728 trimer interface [polypeptide binding]; other site 159087006729 active site 159087006730 substrate binding site [chemical binding]; other site 159087006731 CoA binding site [chemical binding]; other site 159087006732 Predicted transcriptional regulator [Transcription]; Region: COG1959 159087006733 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 159087006734 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 159087006735 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 159087006736 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087006737 catalytic residue [active] 159087006738 cysteine desulfurase; Provisional; Region: PRK14012 159087006739 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 159087006740 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087006741 catalytic residue [active] 159087006742 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 159087006743 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 159087006744 trimerization site [polypeptide binding]; other site 159087006745 active site 159087006746 iron-sulfur cluster assembly protein; Provisional; Region: iscA; PRK09502 159087006747 co-chaperone HscB; Provisional; Region: hscB; PRK03578 159087006748 DnaJ domain; Region: DnaJ; pfam00226 159087006749 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 159087006750 chaperone protein HscA; Provisional; Region: hscA; PRK05183 159087006751 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 159087006752 nucleotide binding site [chemical binding]; other site 159087006753 putative NEF/HSP70 interaction site [polypeptide binding]; other site 159087006754 SBD interface [polypeptide binding]; other site 159087006755 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 159087006756 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 159087006757 catalytic loop [active] 159087006758 iron binding site [ion binding]; other site 159087006759 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 159087006760 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; pfam09996 159087006761 Flagellin N-methylase; Region: FliB; pfam03692 159087006762 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 159087006763 LytTr DNA-binding domain; Region: LytTR; cl04498 159087006764 Domain of unknown function (DUF4072); Region: DUF4072; pfam13284 159087006765 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 159087006766 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 159087006767 motif II; other site 159087006768 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 159087006769 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 159087006770 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 159087006771 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 159087006772 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 159087006773 ATP binding site [chemical binding]; other site 159087006774 putative Mg++ binding site [ion binding]; other site 159087006775 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 159087006776 nucleotide binding region [chemical binding]; other site 159087006777 ATP-binding site [chemical binding]; other site 159087006778 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 159087006779 nucleotide sugar dehydrogenase; Region: NDP-sugDHase; TIGR03026 159087006780 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 159087006781 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 159087006782 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 159087006783 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 159087006784 FeS/SAM binding site; other site 159087006785 AmmeMemoRadiSam system protein A; Region: AmmeMemoSam_A; TIGR04335 159087006786 AMMECR1; Region: AMMECR1; pfam01871 159087006787 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 159087006788 putative ligand binding pocket/active site [active] 159087006789 putative metal binding site [ion binding]; other site 159087006790 MgtC family; Region: MgtC; pfam02308 159087006791 Predicted membrane protein [Function unknown]; Region: COG3174 159087006792 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 159087006793 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 159087006794 substrate binding site; other site 159087006795 dimer interface; other site 159087006796 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 159087006797 homotrimer interaction site [polypeptide binding]; other site 159087006798 zinc binding site [ion binding]; other site 159087006799 CDP-binding sites; other site 159087006800 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 159087006801 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 159087006802 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 159087006803 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087006804 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 159087006805 active site 159087006806 phosphorylation site [posttranslational modification] 159087006807 intermolecular recognition site; other site 159087006808 dimerization interface [polypeptide binding]; other site 159087006809 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 159087006810 PAS fold; Region: PAS_3; pfam08447 159087006811 putative active site [active] 159087006812 heme pocket [chemical binding]; other site 159087006813 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087006814 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006815 metal binding site [ion binding]; metal-binding site 159087006816 active site 159087006817 I-site; other site 159087006818 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 159087006819 HDOD domain; Region: HDOD; pfam08668 159087006820 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087006821 Zn2+ binding site [ion binding]; other site 159087006822 Mg2+ binding site [ion binding]; other site 159087006823 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087006824 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 159087006825 dimerization interface [polypeptide binding]; other site 159087006826 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 159087006827 dimer interface [polypeptide binding]; other site 159087006828 phosphorylation site [posttranslational modification] 159087006829 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 159087006830 ATP binding site [chemical binding]; other site 159087006831 Mg2+ binding site [ion binding]; other site 159087006832 G-X-G motif; other site 159087006833 osmolarity response regulator; Provisional; Region: ompR; PRK09468 159087006834 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 159087006835 active site 159087006836 phosphorylation site [posttranslational modification] 159087006837 intermolecular recognition site; other site 159087006838 dimerization interface [polypeptide binding]; other site 159087006839 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 159087006840 DNA binding site [nucleotide binding] 159087006841 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 159087006842 Glycoprotease family; Region: Peptidase_M22; pfam00814 159087006843 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 159087006844 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087006845 Coenzyme A binding pocket [chemical binding]; other site 159087006846 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 159087006847 Fe-S cluster binding site [ion binding]; other site 159087006848 active site 159087006849 lysophospholipid transporter LplT; Provisional; Region: PRK11195 159087006850 LysR transcriptional regulator; Provisional; Region: rbcR; CHL00180 159087006851 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087006852 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 159087006853 putative dimerization interface [polypeptide binding]; other site 159087006854 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 159087006855 alanine racemase; Reviewed; Region: dadX; PRK03646 159087006856 active site 159087006857 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087006858 substrate binding site [chemical binding]; other site 159087006859 catalytic residues [active] 159087006860 dimer interface [polypeptide binding]; other site 159087006861 DNA repair protein RadA; Provisional; Region: PRK11823 159087006862 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 159087006863 Walker A motif/ATP binding site; other site 159087006864 ATP binding site [chemical binding]; other site 159087006865 Walker B motif; other site 159087006866 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 159087006867 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087006868 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087006869 metal binding site [ion binding]; metal-binding site 159087006870 active site 159087006871 I-site; other site 159087006872 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 159087006873 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 159087006874 FtsX-like permease family; Region: FtsX; pfam02687 159087006875 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 159087006876 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; cl00075 159087006877 FecR protein; Region: FecR; pfam04773 159087006878 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087006879 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087006880 ligand binding site [chemical binding]; other site 159087006881 CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria; Region: CHASE2; smart01080 159087006882 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 159087006883 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 159087006884 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 159087006885 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 159087006886 anti sigma factor interaction site; other site 159087006887 regulatory phosphorylation site [posttranslational modification]; other site 159087006888 hypothetical protein; Provisional; Region: PRK01254 159087006889 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 159087006890 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 159087006891 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 159087006892 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 159087006893 apolar tunnel; other site 159087006894 heme binding site [chemical binding]; other site 159087006895 dimerization interface [polypeptide binding]; other site 159087006896 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 159087006897 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 159087006898 G1 box; other site 159087006899 putative GEF interaction site [polypeptide binding]; other site 159087006900 GTP/Mg2+ binding site [chemical binding]; other site 159087006901 Switch I region; other site 159087006902 G2 box; other site 159087006903 G3 box; other site 159087006904 Switch II region; other site 159087006905 G4 box; other site 159087006906 G5 box; other site 159087006907 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 159087006908 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 159087006909 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 159087006910 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 159087006911 FeS/SAM binding site; other site 159087006912 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 159087006913 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 159087006914 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 159087006915 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 159087006916 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087006917 homodimer interface [polypeptide binding]; other site 159087006918 catalytic residue [active] 159087006919 Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes; Region: Motor_domain; cl00286 159087006920 excinuclease ABC subunit B; Provisional; Region: PRK05298 159087006921 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 159087006922 ATP-binding site [chemical binding]; other site 159087006923 ATP binding site [chemical binding]; other site 159087006924 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 159087006925 nucleotide binding region [chemical binding]; other site 159087006926 ATP-binding site [chemical binding]; other site 159087006927 Ultra-violet resistance protein B; Region: UvrB; pfam12344 159087006928 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 159087006929 Low molecular weight phosphatase family; Region: LMWPc; cd00115 159087006930 active site 159087006931 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 159087006932 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 159087006933 homodimer interface [polypeptide binding]; other site 159087006934 oligonucleotide binding site [chemical binding]; other site 159087006935 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 159087006936 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 159087006937 RNA binding surface [nucleotide binding]; other site 159087006938 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 159087006939 active site 159087006940 Ferredoxin subunits of nitrite reductase and ring-hydroxylating dioxygenases [Inorganic ion transport and metabolism / General function prediction only]; Region: {NirD}; COG2146 159087006941 iron-sulfur cluster [ion binding]; other site 159087006942 [2Fe-2S] cluster binding site [ion binding]; other site 159087006943 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 159087006944 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 159087006945 tandem repeat interface [polypeptide binding]; other site 159087006946 oligomer interface [polypeptide binding]; other site 159087006947 active site residues [active] 159087006948 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 159087006949 putative SAM binding site [chemical binding]; other site 159087006950 homodimer interface [polypeptide binding]; other site 159087006951 Maf-like protein; Region: Maf; pfam02545 159087006952 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 159087006953 active site 159087006954 dimer interface [polypeptide binding]; other site 159087006955 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 159087006956 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 159087006957 putative phosphate acyltransferase; Provisional; Region: PRK05331 159087006958 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 159087006959 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 159087006960 dimer interface [polypeptide binding]; other site 159087006961 active site 159087006962 CoA binding pocket [chemical binding]; other site 159087006963 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 159087006964 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 159087006965 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 159087006966 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 159087006967 NAD(P) binding site [chemical binding]; other site 159087006968 homotetramer interface [polypeptide binding]; other site 159087006969 homodimer interface [polypeptide binding]; other site 159087006970 active site 159087006971 acyl carrier protein; Provisional; Region: acpP; PRK00982 159087006972 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 159087006973 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 159087006974 dimer interface [polypeptide binding]; other site 159087006975 active site 159087006976 L-aspartate oxidase; Provisional; Region: PRK09077 159087006977 L-aspartate oxidase; Provisional; Region: PRK06175 159087006978 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 159087006979 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 159087006980 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087006981 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 159087006982 DNA binding residues [nucleotide binding] 159087006983 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 159087006984 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 159087006985 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 159087006986 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 159087006987 protein binding site [polypeptide binding]; other site 159087006988 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 159087006989 protein binding site [polypeptide binding]; other site 159087006990 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 159087006991 GTP-binding protein LepA; Provisional; Region: PRK05433 159087006992 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 159087006993 G1 box; other site 159087006994 putative GEF interaction site [polypeptide binding]; other site 159087006995 GTP/Mg2+ binding site [chemical binding]; other site 159087006996 Switch I region; other site 159087006997 G2 box; other site 159087006998 G3 box; other site 159087006999 Switch II region; other site 159087007000 G4 box; other site 159087007001 G5 box; other site 159087007002 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 159087007003 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 159087007004 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 159087007005 signal peptidase I; Provisional; Region: PRK10861 159087007006 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 159087007007 Catalytic site [active] 159087007008 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 159087007009 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 159087007010 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 159087007011 dimerization interface [polypeptide binding]; other site 159087007012 active site 159087007013 metal binding site [ion binding]; metal-binding site 159087007014 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 159087007015 dsRNA binding site [nucleotide binding]; other site 159087007016 GTPase Era; Reviewed; Region: era; PRK00089 159087007017 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 159087007018 G1 box; other site 159087007019 GTP/Mg2+ binding site [chemical binding]; other site 159087007020 Switch I region; other site 159087007021 G2 box; other site 159087007022 Switch II region; other site 159087007023 G3 box; other site 159087007024 G4 box; other site 159087007025 G5 box; other site 159087007026 KH domain; Region: KH_2; pfam07650 159087007027 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 159087007028 Recombination protein O N terminal; Region: RecO_N; pfam11967 159087007029 Recombination protein O C terminal; Region: RecO_C; pfam02565 159087007030 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 159087007031 active site 159087007032 hydrophilic channel; other site 159087007033 dimerization interface [polypeptide binding]; other site 159087007034 catalytic residues [active] 159087007035 active site lid [active] 159087007036 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 159087007037 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 159087007038 beta-hexosaminidase; Provisional; Region: PRK05337 159087007039 elongation factor P; Validated; Region: PRK00529 159087007040 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 159087007041 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 159087007042 RNA binding site [nucleotide binding]; other site 159087007043 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 159087007044 RNA binding site [nucleotide binding]; other site 159087007045 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 159087007046 conserved hypothetical protein, PP_1857 family; Region: efp_adjacent_2; TIGR03837 159087007047 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 159087007048 Fe-S cluster binding site [ion binding]; other site 159087007049 DNA binding site [nucleotide binding] 159087007050 active site 159087007051 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 159087007052 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 159087007053 GIY-YIG motif/motif A; other site 159087007054 active site 159087007055 catalytic site [active] 159087007056 putative DNA binding site [nucleotide binding]; other site 159087007057 metal binding site [ion binding]; metal-binding site 159087007058 UvrB/uvrC motif; Region: UVR; pfam02151 159087007059 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 159087007060 Helix-hairpin-helix motif; Region: HHH; pfam00633 159087007061 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 159087007062 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 159087007063 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 159087007064 Transposase; Region: DEDD_Tnp_IS110; pfam01548 159087007065 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 159087007066 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087007067 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 159087007068 ligand binding site [chemical binding]; other site 159087007069 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 159087007070 non-specific DNA interactions [nucleotide binding]; other site 159087007071 DNA binding site [nucleotide binding] 159087007072 sequence specific DNA binding site [nucleotide binding]; other site 159087007073 putative cAMP binding site [chemical binding]; other site 159087007074 PAS domain; Region: PAS_9; pfam13426 159087007075 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 159087007076 CheB methylesterase; Region: CheB_methylest; pfam01339 159087007077 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 159087007078 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 159087007079 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 159087007080 PAS domain; Region: PAS_10; pfam13596 159087007081 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 159087007082 Putative glucoamylase; Region: Glycoamylase; pfam10091 159087007083 Second GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_2_like; cd11753 159087007084 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 159087007085 First GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_1_like; cd11756 159087007086 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 159087007087 BON domain; Region: BON; pfam04972 159087007088 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087007089 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 159087007090 active site 159087007091 phosphorylation site [posttranslational modification] 159087007092 intermolecular recognition site; other site 159087007093 PAS domain S-box; Region: sensory_box; TIGR00229 159087007094 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 159087007095 putative active site [active] 159087007096 heme pocket [chemical binding]; other site 159087007097 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 159087007098 PAS domain; Region: PAS_9; pfam13426 159087007099 putative active site [active] 159087007100 heme pocket [chemical binding]; other site 159087007101 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087007102 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087007103 metal binding site [ion binding]; metal-binding site 159087007104 active site 159087007105 I-site; other site 159087007106 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 159087007107 Uncharacterized conserved protein [Function unknown]; Region: COG3461 159087007108 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 159087007109 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 159087007110 periplasmic protein; Provisional; Region: PRK10568 159087007111 BON domain; Region: BON; pfam04972 159087007112 transcription termination factor Rho; Provisional; Region: PRK12678 159087007113 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 159087007114 putative amphipathic alpha helix; other site 159087007115 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 159087007116 HSP70 interaction site [polypeptide binding]; other site 159087007117 Esterase PHB depolymerase; Region: Esterase_phd; pfam10503 159087007118 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 159087007119 CsbD-like; Region: CsbD; pfam05532 159087007120 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 159087007121 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 159087007122 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 159087007123 putative active site [active] 159087007124 transaldolase; Provisional; Region: PRK03903 159087007125 catalytic residue [active] 159087007126 putative phosphoketolase; Provisional; Region: PRK05261 159087007127 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 159087007128 TPP-binding site; other site 159087007129 XFP C-terminal domain; Region: XFP_C; pfam09363 159087007130 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 159087007131 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 159087007132 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 159087007133 HSP70 interaction site [polypeptide binding]; other site 159087007134 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 159087007135 substrate binding site [polypeptide binding]; other site 159087007136 dimer interface [polypeptide binding]; other site 159087007137 A domain in the BMP inhibitor chordin and in microbial proteins; Region: CHRD; smart00754 159087007138 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 159087007139 NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11; Region: ALDH_F11_NP-GAPDH; cd07082 159087007140 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 159087007141 tetrameric interface [polypeptide binding]; other site 159087007142 activator binding site; other site 159087007143 NADP binding site [chemical binding]; other site 159087007144 substrate binding site [chemical binding]; other site 159087007145 catalytic residues [active] 159087007146 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 159087007147 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 159087007148 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 159087007149 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 159087007150 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 159087007151 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 159087007152 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 159087007153 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 159087007154 putative active site [active] 159087007155 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087007156 Predicted flavoprotein [General function prediction only]; Region: COG0431 159087007157 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 159087007158 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_6; cd07824 159087007159 putative hydrophobic ligand binding site [chemical binding]; other site 159087007160 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 159087007161 BON domain; Region: BON; pfam04972 159087007162 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 159087007163 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 159087007164 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087007165 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 159087007166 Soluble P-type ATPase [General function prediction only]; Region: COG4087 159087007167 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 159087007168 cyclase homology domain; Region: CHD; cd07302 159087007169 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 159087007170 nucleotidyl binding site; other site 159087007171 metal binding site [ion binding]; metal-binding site 159087007172 dimer interface [polypeptide binding]; other site 159087007173 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 159087007174 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 159087007175 phosphopeptide binding site; other site 159087007176 Small integral membrane protein [Function unknown]; Region: COG5487; cl17674 159087007177 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 159087007178 putative active site [active] 159087007179 catalytic site [active] 159087007180 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 159087007181 putative active site [active] 159087007182 catalytic site [active] 159087007183 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 159087007184 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 159087007185 dimerization interface [polypeptide binding]; other site 159087007186 substrate binding site [chemical binding]; other site 159087007187 active site 159087007188 calcium binding site [ion binding]; other site 159087007189 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 159087007190 active site clefts [active] 159087007191 zinc binding site [ion binding]; other site 159087007192 dimer interface [polypeptide binding]; other site 159087007193 Bacterial protein of unknown function (DUF937); Region: DUF937; pfam06078 159087007194 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 159087007195 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 159087007196 active site 159087007197 phosphorylation site [posttranslational modification] 159087007198 intermolecular recognition site; other site 159087007199 dimerization interface [polypeptide binding]; other site 159087007200 LytTr DNA-binding domain; Region: LytTR; smart00850 159087007201 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 159087007202 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 159087007203 GAF domain; Region: GAF; pfam01590 159087007204 Histidine kinase; Region: His_kinase; pfam06580 159087007205 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 159087007206 ATP binding site [chemical binding]; other site 159087007207 Mg2+ binding site [ion binding]; other site 159087007208 G-X-G motif; other site 159087007209 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 159087007210 Carbon starvation protein CstA; Region: CstA; pfam02554 159087007211 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 159087007212 Pyruvate formate lyase 1; Region: PFL1; cd01678 159087007213 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 159087007214 coenzyme A binding site [chemical binding]; other site 159087007215 active site 159087007216 catalytic residues [active] 159087007217 glycine loop; other site 159087007218 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 159087007219 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 159087007220 FeS/SAM binding site; other site 159087007221 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 159087007222 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 159087007223 dimer interaction site [polypeptide binding]; other site 159087007224 substrate-binding tunnel; other site 159087007225 active site 159087007226 catalytic site [active] 159087007227 substrate binding site [chemical binding]; other site 159087007228 phosphate acetyltransferase; Provisional; Region: PRK11890 159087007229 propionate/acetate kinase; Provisional; Region: PRK12379 159087007230 Acetokinase family; Region: Acetate_kinase; cl17229 159087007231 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 159087007232 Protein of unknown function (DUF3348); Region: DUF3348; pfam11828 159087007233 Domain of unknown function (DUF802); Region: DUF802; pfam05650 159087007234 Domain of unknown function (DUF802); Region: DUF802; pfam05650 159087007235 hypothetical protein; Provisional; Region: PRK09040 159087007236 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087007237 ligand binding site [chemical binding]; other site 159087007238 Protein of unknown function (DUF2894); Region: DUF2894; pfam11445 159087007239 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 159087007240 PAS domain; Region: PAS_9; pfam13426 159087007241 putative active site [active] 159087007242 heme pocket [chemical binding]; other site 159087007243 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 159087007244 dimer interface [polypeptide binding]; other site 159087007245 phosphorylation site [posttranslational modification] 159087007246 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 159087007247 ATP binding site [chemical binding]; other site 159087007248 Mg2+ binding site [ion binding]; other site 159087007249 G-X-G motif; other site 159087007250 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087007251 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 159087007252 active site 159087007253 phosphorylation site [posttranslational modification] 159087007254 intermolecular recognition site; other site 159087007255 dimerization interface [polypeptide binding]; other site 159087007256 Response regulator receiver domain; Region: Response_reg; pfam00072 159087007257 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 159087007258 active site 159087007259 phosphorylation site [posttranslational modification] 159087007260 intermolecular recognition site; other site 159087007261 dimerization interface [polypeptide binding]; other site 159087007262 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 159087007263 haemagglutination activity domain; Region: Haemagg_act; smart00912 159087007264 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 159087007265 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 159087007266 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 159087007267 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 159087007268 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 159087007269 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 159087007270 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087007271 ligand binding site [chemical binding]; other site 159087007272 Transcriptional regulators [Transcription]; Region: MarR; COG1846 159087007273 MarR family; Region: MarR_2; pfam12802 159087007274 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087007275 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 159087007276 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 159087007277 Peptidase C26; Region: Peptidase_C26; pfam07722 159087007278 catalytic triad [active] 159087007279 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 159087007280 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 159087007281 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 159087007282 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 159087007283 Beta-lactamase; Region: Beta-lactamase; pfam00144 159087007284 hypothetical protein; Provisional; Region: PRK10621 159087007285 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087007286 pyruvate kinase; Provisional; Region: PRK06247 159087007287 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 159087007288 domain interfaces; other site 159087007289 active site 159087007290 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 159087007291 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 159087007292 MOFRL family; Region: MOFRL; pfam05161 159087007293 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 159087007294 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 159087007295 putative substrate translocation pore; other site 159087007296 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 159087007297 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 159087007298 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 159087007299 active site 159087007300 DNA binding site [nucleotide binding] 159087007301 RNA polymerase sigma factor; Provisional; Region: PRK11922 159087007302 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087007303 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 159087007304 DNA binding residues [nucleotide binding] 159087007305 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 159087007306 Ferritin-like domain; Region: Ferritin; pfam00210 159087007307 dinuclear metal binding motif [ion binding]; other site 159087007308 Cytochrome c2 [Energy production and conversion]; Region: COG3474 159087007309 PAS domain S-box; Region: sensory_box; TIGR00229 159087007310 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 159087007311 putative active site [active] 159087007312 heme pocket [chemical binding]; other site 159087007313 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087007314 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087007315 metal binding site [ion binding]; metal-binding site 159087007316 active site 159087007317 I-site; other site 159087007318 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 159087007319 Predicted esterase [General function prediction only]; Region: COG0400 159087007320 putative hydrolase; Provisional; Region: PRK11460 159087007321 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 159087007322 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 159087007323 dimerization interface [polypeptide binding]; other site 159087007324 putative Zn2+ binding site [ion binding]; other site 159087007325 putative DNA binding site [nucleotide binding]; other site 159087007326 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 159087007327 substrate binding site [chemical binding]; other site 159087007328 dimerization interface [polypeptide binding]; other site 159087007329 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 159087007330 active site 159087007331 catalytic residues [active] 159087007332 metal binding site [ion binding]; metal-binding site 159087007333 Serine hydrolase; Region: Ser_hydrolase; pfam06821 159087007334 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087007335 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 159087007336 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 159087007337 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 159087007338 dimerization interface [polypeptide binding]; other site 159087007339 putative DNA binding site [nucleotide binding]; other site 159087007340 putative Zn2+ binding site [ion binding]; other site 159087007341 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 159087007342 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 159087007343 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 159087007344 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 159087007345 dimer interface [polypeptide binding]; other site 159087007346 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087007347 catalytic residue [active] 159087007348 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 159087007349 active site residue [active] 159087007350 Putative serine esterase (DUF676); Region: DUF676; pfam05057 159087007351 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087007352 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 159087007353 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 159087007354 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 159087007355 hexamer interface [polypeptide binding]; other site 159087007356 ligand binding site [chemical binding]; other site 159087007357 putative active site [active] 159087007358 NAD(P) binding site [chemical binding]; other site 159087007359 carboxy-terminal protease; Provisional; Region: PRK11186 159087007360 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 159087007361 protein binding site [polypeptide binding]; other site 159087007362 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 159087007363 Catalytic dyad [active] 159087007364 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 159087007365 Alpha/beta hydrolase of unknown function (DUF1057); Region: DUF1057; pfam06342 159087007366 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087007367 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087007368 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 159087007369 active site 159087007370 phosphorylation site [posttranslational modification] 159087007371 intermolecular recognition site; other site 159087007372 dimerization interface [polypeptide binding]; other site 159087007373 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 159087007374 Walker A motif; other site 159087007375 ATP binding site [chemical binding]; other site 159087007376 Walker B motif; other site 159087007377 arginine finger; other site 159087007378 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 159087007379 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 159087007380 putative substrate binding pocket [chemical binding]; other site 159087007381 trimer interface [polypeptide binding]; other site 159087007382 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 159087007383 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 159087007384 dimer interface [polypeptide binding]; other site 159087007385 phosphorylation site [posttranslational modification] 159087007386 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 159087007387 ATP binding site [chemical binding]; other site 159087007388 Mg2+ binding site [ion binding]; other site 159087007389 G-X-G motif; other site 159087007390 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 159087007391 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 159087007392 Walker A/P-loop; other site 159087007393 ATP binding site [chemical binding]; other site 159087007394 Q-loop/lid; other site 159087007395 ABC transporter signature motif; other site 159087007396 Walker B; other site 159087007397 D-loop; other site 159087007398 H-loop/switch region; other site 159087007399 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 159087007400 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 159087007401 dimer interface [polypeptide binding]; other site 159087007402 conserved gate region; other site 159087007403 putative PBP binding loops; other site 159087007404 ABC-ATPase subunit interface; other site 159087007405 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 159087007406 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 159087007407 substrate binding pocket [chemical binding]; other site 159087007408 membrane-bound complex binding site; other site 159087007409 DnaJ domain; Region: DnaJ; pfam00226 159087007410 Bacterial protein of unknown function (DUF898); Region: DUF898; pfam05987 159087007411 Peptidase family M48; Region: Peptidase_M48; cl12018 159087007412 Domain of unknown function DUF302; Region: DUF302; pfam03625 159087007413 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 159087007414 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 159087007415 dimer interface [polypeptide binding]; other site 159087007416 active site 159087007417 metal binding site [ion binding]; metal-binding site 159087007418 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087007419 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 159087007420 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 159087007421 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 159087007422 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087007423 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 159087007424 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 159087007425 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 159087007426 Protein of unknown function (DUF3304); Region: DUF3304; pfam11745 159087007427 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 159087007428 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 159087007429 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 159087007430 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087007431 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 159087007432 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; pfam10106 159087007433 Domain of unknown function (DUF4285); Region: DUF4285; pfam14113 159087007434 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 159087007435 Clp amino terminal domain; Region: Clp_N; pfam02861 159087007436 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 159087007437 Walker A motif; other site 159087007438 ATP binding site [chemical binding]; other site 159087007439 Walker B motif; other site 159087007440 arginine finger; other site 159087007441 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 159087007442 Walker A motif; other site 159087007443 ATP binding site [chemical binding]; other site 159087007444 Walker B motif; other site 159087007445 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 159087007446 type VI secretion protein, VC_A0111 family; Region: VI_chp_1; TIGR03347 159087007447 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 159087007448 type VI secretion protein, VC_A0110 family; Region: VI_chp_6; TIGR03359 159087007449 type VI secretion system lysozyme-like protein; Region: VI_zyme; TIGR03357 159087007450 Protein of unknown function (DUF796); Region: DUF796; pfam05638 159087007451 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 159087007452 Protein of unknown function (DUF877); Region: DUF877; pfam05943 159087007453 Protein of unknown function (DUF770); Region: DUF770; pfam05591 159087007454 Tetratricopeptide repeat; Region: TPR_16; pfam13432 159087007455 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 159087007456 TPR motif; other site 159087007457 binding surface 159087007458 Type VI secretion lipoprotein; Region: T6SS-SciN; pfam12790 159087007459 type VI secretion protein, VC_A0114 family; Region: VI_chp_4; TIGR03353 159087007460 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 159087007461 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 159087007462 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 159087007463 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 159087007464 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087007465 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 159087007466 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; pfam10106 159087007467 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 159087007468 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 159087007469 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087007470 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087007471 ligand binding site [chemical binding]; other site 159087007472 type VI secretion-associated protein, BMA_A0400 family; Region: VI_minor_4; TIGR03373 159087007473 Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]; Region: IcmF; COG3523 159087007474 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 159087007475 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 159087007476 PAAR motif; Region: PAAR_motif; pfam05488 159087007477 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 159087007478 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_M15_4; pfam13539 159087007479 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087007480 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 159087007481 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087007482 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 159087007483 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 159087007484 active site 159087007485 PilZ domain; Region: PilZ; cl01260 159087007486 DNA polymerase III subunit delta'; Validated; Region: PRK06964 159087007487 DNA polymerase III subunit delta'; Validated; Region: PRK08485 159087007488 thymidylate kinase; Validated; Region: tmk; PRK00698 159087007489 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 159087007490 TMP-binding site; other site 159087007491 ATP-binding site [chemical binding]; other site 159087007492 YceG-like family; Region: YceG; pfam02618 159087007493 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 159087007494 dimerization interface [polypeptide binding]; other site 159087007495 Aminomethyltransferase folate-binding domain; Region: GCV_T; pfam01571 159087007496 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 159087007497 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 159087007498 NRDE protein; Region: NRDE; cl01315 159087007499 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 159087007500 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 159087007501 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 159087007502 nucleoside/Zn binding site; other site 159087007503 dimer interface [polypeptide binding]; other site 159087007504 catalytic motif [active] 159087007505 TIR domain; Region: TIR_2; pfam13676 159087007506 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 159087007507 active site 159087007508 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 159087007509 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 159087007510 Uncharacterized protein conserved in bacteria (DUF2186); Region: DUF2186; pfam09952 159087007511 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 159087007512 PRTRC system protein D; Region: PRTRC_D; TIGR03739 159087007513 Plasmid segregation protein ParM and similar proteins; Region: ParM_like; cd10227 159087007514 Mg binding site [ion binding]; other site 159087007515 nucleotide binding site [chemical binding]; other site 159087007516 putative protofilament interface [polypeptide binding]; other site 159087007517 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 159087007518 Integrase; Region: Integrase_1; pfam12835 159087007519 ParB-like nuclease domain; Region: ParBc; pfam02195 159087007520 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087007521 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087007522 metal binding site [ion binding]; metal-binding site 159087007523 active site 159087007524 I-site; other site 159087007525 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 159087007526 S-adenosylmethionine binding site [chemical binding]; other site 159087007527 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 159087007528 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 159087007529 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 159087007530 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087007531 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 159087007532 helicase superfamily c-terminal domain; Region: HELICc; smart00490 159087007533 Domain of unknown function (DUF4372); Region: DUF4372; pfam14294 159087007534 FOG: Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3385 159087007535 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 159087007536 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 159087007537 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 159087007538 MPN+ (JAMM) motif; other site 159087007539 Zinc-binding site [ion binding]; other site 159087007540 Competence protein CoiA-like family; Region: CoiA; cl11541 159087007541 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 159087007542 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087007543 Walker A/P-loop; other site 159087007544 ATP binding site [chemical binding]; other site 159087007545 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087007546 ABC transporter signature motif; other site 159087007547 Walker B; other site 159087007548 D-loop; other site 159087007549 H-loop/switch region; other site 159087007550 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 159087007551 active site 159087007552 metal binding site [ion binding]; metal-binding site 159087007553 Family description; Region: UvrD_C_2; pfam13538 159087007554 AAA-like domain; Region: AAA_10; pfam12846 159087007555 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 159087007556 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 159087007557 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 159087007558 active site 159087007559 catalytic residues [active] 159087007560 Int/Topo IB signature motif; other site 159087007561 DNA binding site [nucleotide binding] 159087007562 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 159087007563 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 159087007564 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 159087007565 non-specific DNA binding site [nucleotide binding]; other site 159087007566 salt bridge; other site 159087007567 sequence-specific DNA binding site [nucleotide binding]; other site 159087007568 Predicted membrane protein [Function unknown]; Region: COG2119 159087007569 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 159087007570 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 159087007571 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 159087007572 EamA-like transporter family; Region: EamA; pfam00892 159087007573 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 159087007574 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 159087007575 putative active site [active] 159087007576 putative NTP binding site [chemical binding]; other site 159087007577 putative nucleic acid binding site [nucleotide binding]; other site 159087007578 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 159087007579 Nitrogen regulatory protein P-II; Region: P-II; cl00412 159087007580 Nitrogen regulatory protein P-II; Region: P-II; smart00938 159087007581 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087007582 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087007583 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087007584 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087007585 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087007586 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 159087007587 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 159087007588 DNA binding residues [nucleotide binding] 159087007589 dimer interface [polypeptide binding]; other site 159087007590 putative metal binding site [ion binding]; other site 159087007591 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087007592 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; cl00207 159087007593 metal-binding site [ion binding] 159087007594 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087007595 Soluble P-type ATPase [General function prediction only]; Region: COG4087 159087007596 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 159087007597 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 159087007598 dimerization interface [polypeptide binding]; other site 159087007599 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 159087007600 dimer interface [polypeptide binding]; other site 159087007601 phosphorylation site [posttranslational modification] 159087007602 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 159087007603 ATP binding site [chemical binding]; other site 159087007604 Mg2+ binding site [ion binding]; other site 159087007605 G-X-G motif; other site 159087007606 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 159087007607 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 159087007608 active site 159087007609 phosphorylation site [posttranslational modification] 159087007610 intermolecular recognition site; other site 159087007611 dimerization interface [polypeptide binding]; other site 159087007612 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 159087007613 DNA binding site [nucleotide binding] 159087007614 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 159087007615 Predicted metal-binding protein [General function prediction only]; Region: COG3019 159087007616 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 159087007617 Outer membrane efflux protein; Region: OEP; pfam02321 159087007618 Outer membrane efflux protein; Region: OEP; pfam02321 159087007619 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087007620 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087007621 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 159087007622 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087007623 YHS domain; Region: YHS; pfam04945 159087007624 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087007625 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087007626 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 159087007627 motif II; other site 159087007628 Hemerythrin; Region: Hemerythrin; cd12107 159087007629 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 159087007630 Flagellar basal body protein [Cell motility and secretion]; Region: FlgB; COG1815 159087007631 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 159087007632 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087007633 Zn2+ binding site [ion binding]; other site 159087007634 Mg2+ binding site [ion binding]; other site 159087007635 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 159087007636 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 159087007637 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 159087007638 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 159087007639 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 159087007640 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 159087007641 tetrahydromethanopterin S-methyltransferase subunit A; Provisional; Region: PRK00964 159087007642 Tetrahydromethanopterin S-methyltransferase, subunit A; Region: MtrA; cl04449 159087007643 Domain of unknown function (DUF4346); Region: DUF4346; pfam14251 159087007644 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 159087007645 dimerization interface [polypeptide binding]; other site 159087007646 putative DNA binding site [nucleotide binding]; other site 159087007647 putative Zn2+ binding site [ion binding]; other site 159087007648 Copper resistance protein K; Region: CopK; pfam11525 159087007649 putative transposase OrfB; Reviewed; Region: PHA02517 159087007650 HTH-like domain; Region: HTH_21; pfam13276 159087007651 Integrase core domain; Region: rve; pfam00665 159087007652 Integrase core domain; Region: rve_3; pfam13683 159087007653 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 159087007654 ATP binding site [chemical binding]; other site 159087007655 Mg2+ binding site [ion binding]; other site 159087007656 G-X-G motif; other site 159087007657 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 159087007658 Zinc-binding domain of primase-helicase; Region: Prim_Zn_Ribbon; smart00778 159087007659 CHC2 zinc finger; Region: zf-CHC2; cl17510 159087007660 Toprim domain; Region: Toprim_3; pfam13362 159087007661 active site 159087007662 metal binding site [ion binding]; metal-binding site 159087007663 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 159087007664 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087007665 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087007666 metal binding site [ion binding]; metal-binding site 159087007667 active site 159087007668 I-site; other site 159087007669 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 159087007670 non-specific DNA binding site [nucleotide binding]; other site 159087007671 salt bridge; other site 159087007672 sequence-specific DNA binding site [nucleotide binding]; other site 159087007673 Predicted membrane protein [Function unknown]; Region: COG2510 159087007674 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 159087007675 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 159087007676 dimer interface [polypeptide binding]; other site 159087007677 phosphorylation site [posttranslational modification] 159087007678 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 159087007679 ATP binding site [chemical binding]; other site 159087007680 Mg2+ binding site [ion binding]; other site 159087007681 G-X-G motif; other site 159087007682 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087007683 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 159087007684 active site 159087007685 phosphorylation site [posttranslational modification] 159087007686 intermolecular recognition site; other site 159087007687 dimerization interface [polypeptide binding]; other site 159087007688 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 159087007689 DNA binding site [nucleotide binding] 159087007690 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007691 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007692 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007693 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4705 159087007694 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007695 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007696 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007697 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 159087007698 PAP2_like proteins, BcrC_like subfamily. Several members of this family have been annotated as bacitracin transport permeases, as it was suspected that they form the permease component of an ABC transporter system. It was shown, however, that BcrC from...; Region: PAP2_BcrC_like; cd03385 159087007699 active site 159087007700 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 159087007701 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 159087007702 Putative helicase; Region: TraI_2; pfam07514 159087007703 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 159087007704 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 159087007705 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 159087007706 Domain of unknown function (DUF4400); Region: DUF4400; pfam14348 159087007707 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 159087007708 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 159087007709 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087007710 catalytic residue [active] 159087007711 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087007712 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087007713 ligand binding site [chemical binding]; other site 159087007714 TraL protein; Region: TraL; pfam07178 159087007715 type IV conjugative transfer system protein TraE; Region: TraE_TIGR; TIGR02761 159087007716 TraK protein; Region: TraK; pfam06586 159087007717 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 159087007718 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 159087007719 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 159087007720 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 159087007721 dimerization domain [polypeptide binding]; other site 159087007722 dimer interface [polypeptide binding]; other site 159087007723 catalytic residues [active] 159087007724 type IV conjugative transfer system lipoprotein TraV; Region: TraV; TIGR02747 159087007725 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 159087007726 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 159087007727 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 159087007728 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 159087007729 Walker A motif; other site 159087007730 ATP binding site [chemical binding]; other site 159087007731 conjugative transfer signal peptidase TraF; Region: TraF_Ti; TIGR02771 159087007732 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 159087007733 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 159087007734 TraU protein; Region: TraU; pfam06834 159087007735 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; pfam09673 159087007736 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 159087007737 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 159087007738 TraF-like protein; Region: TraF-like; TIGR02740 159087007739 F plasmid transfer operon protein; Region: TraF; pfam13728 159087007740 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 159087007741 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 159087007742 conjugal transfer mating pair stabilization protein TraG; Provisional; Region: PRK13735 159087007743 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 159087007744 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 159087007745 integrase; Provisional; Region: PRK09692 159087007746 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 159087007747 active site 159087007748 Int/Topo IB signature motif; other site 159087007749 GMP synthase; Reviewed; Region: guaA; PRK00074 159087007750 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 159087007751 AMP/PPi binding site [chemical binding]; other site 159087007752 candidate oxyanion hole; other site 159087007753 catalytic triad [active] 159087007754 potential glutamine specificity residues [chemical binding]; other site 159087007755 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 159087007756 ATP Binding subdomain [chemical binding]; other site 159087007757 Ligand Binding sites [chemical binding]; other site 159087007758 Dimerization subdomain; other site 159087007759 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 159087007760 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 159087007761 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 159087007762 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 159087007763 active site 159087007764 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087007765 hypothetical protein; Validated; Region: PRK01777 159087007766 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 159087007767 putative coenzyme Q binding site [chemical binding]; other site 159087007768 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 159087007769 SmpB-tmRNA interface; other site 159087007770 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087007771 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 159087007772 active site 159087007773 phosphorylation site [posttranslational modification] 159087007774 intermolecular recognition site; other site 159087007775 dimerization interface [polypeptide binding]; other site 159087007776 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 159087007777 DNA binding residues [nucleotide binding] 159087007778 dimerization interface [polypeptide binding]; other site 159087007779 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylic-acid synthase; Region: menD; TIGR00173 159087007780 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 159087007781 dimer interface [polypeptide binding]; other site 159087007782 tetramer interface [polypeptide binding]; other site 159087007783 PYR/PP interface [polypeptide binding]; other site 159087007784 TPP binding site [chemical binding]; other site 159087007785 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 159087007786 TPP-binding site; other site 159087007787 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 159087007788 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 159087007789 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 159087007790 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 159087007791 MutS domain I; Region: MutS_I; pfam01624 159087007792 MutS domain II; Region: MutS_II; pfam05188 159087007793 MutS domain III; Region: MutS_III; pfam05192 159087007794 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 159087007795 Walker A/P-loop; other site 159087007796 ATP binding site [chemical binding]; other site 159087007797 Q-loop/lid; other site 159087007798 ABC transporter signature motif; other site 159087007799 Walker B; other site 159087007800 D-loop; other site 159087007801 H-loop/switch region; other site 159087007802 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 159087007803 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 159087007804 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 159087007805 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 159087007806 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 159087007807 substrate binding site [chemical binding]; other site 159087007808 oxyanion hole (OAH) forming residues; other site 159087007809 trimer interface [polypeptide binding]; other site 159087007810 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 159087007811 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087007812 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 159087007813 acyl-CoA synthetase; Validated; Region: PRK08316 159087007814 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087007815 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 159087007816 acyl-activating enzyme (AAE) consensus motif; other site 159087007817 acyl-activating enzyme (AAE) consensus motif; other site 159087007818 putative AMP binding site [chemical binding]; other site 159087007819 putative active site [active] 159087007820 putative CoA binding site [chemical binding]; other site 159087007821 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 159087007822 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 159087007823 dimer interface [polypeptide binding]; other site 159087007824 active site 159087007825 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 159087007826 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 159087007827 active site 159087007828 enoyl-CoA hydratase; Provisional; Region: PRK06688 159087007829 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 159087007830 substrate binding site [chemical binding]; other site 159087007831 oxyanion hole (OAH) forming residues; other site 159087007832 trimer interface [polypeptide binding]; other site 159087007833 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 159087007834 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087007835 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 159087007836 acyl-activating enzyme (AAE) consensus motif; other site 159087007837 putative AMP binding site [chemical binding]; other site 159087007838 putative active site [active] 159087007839 putative CoA binding site [chemical binding]; other site 159087007840 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087007841 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087007842 Walker A/P-loop; other site 159087007843 ATP binding site [chemical binding]; other site 159087007844 Q-loop/lid; other site 159087007845 ABC transporter signature motif; other site 159087007846 Walker B; other site 159087007847 D-loop; other site 159087007848 H-loop/switch region; other site 159087007849 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 159087007850 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 159087007851 putative ligand binding site [chemical binding]; other site 159087007852 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087007853 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087007854 TM-ABC transporter signature motif; other site 159087007855 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087007856 TM-ABC transporter signature motif; other site 159087007857 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 159087007858 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087007859 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087007860 Walker A/P-loop; other site 159087007861 ATP binding site [chemical binding]; other site 159087007862 Q-loop/lid; other site 159087007863 ABC transporter signature motif; other site 159087007864 Walker B; other site 159087007865 D-loop; other site 159087007866 H-loop/switch region; other site 159087007867 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 159087007868 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 159087007869 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087007870 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 159087007871 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 159087007872 catalytic triad [active] 159087007873 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 159087007874 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 159087007875 enolase; Provisional; Region: eno; PRK00077 159087007876 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 159087007877 dimer interface [polypeptide binding]; other site 159087007878 metal binding site [ion binding]; metal-binding site 159087007879 substrate binding pocket [chemical binding]; other site 159087007880 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 159087007881 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 159087007882 CTP synthetase; Validated; Region: pyrG; PRK05380 159087007883 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 159087007884 Catalytic site [active] 159087007885 active site 159087007886 UTP binding site [chemical binding]; other site 159087007887 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 159087007888 active site 159087007889 putative oxyanion hole; other site 159087007890 catalytic triad [active] 159087007891 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 159087007892 "initiating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are...; Region: init_cond_enzymes; cd00827 159087007893 dimer interface [polypeptide binding]; other site 159087007894 active site 159087007895 A predicted NlpC/p60-like peptidase; Region: BtrH; pfam14399 159087007896 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 159087007897 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087007898 Walker A/P-loop; other site 159087007899 ATP binding site [chemical binding]; other site 159087007900 Q-loop/lid; other site 159087007901 ABC transporter signature motif; other site 159087007902 Walker B; other site 159087007903 D-loop; other site 159087007904 H-loop/switch region; other site 159087007905 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 159087007906 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 159087007907 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 159087007908 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 159087007909 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087007910 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 159087007911 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 159087007912 active site 159087007913 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 159087007914 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 159087007915 catalytic residues [active] 159087007916 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 159087007917 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 159087007918 putative active site [active] 159087007919 Zn binding site [ion binding]; other site 159087007920 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 159087007921 dimerization interface [polypeptide binding]; other site 159087007922 PAS domain S-box; Region: sensory_box; TIGR00229 159087007923 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 159087007924 putative active site [active] 159087007925 heme pocket [chemical binding]; other site 159087007926 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 159087007927 dimer interface [polypeptide binding]; other site 159087007928 phosphorylation site [posttranslational modification] 159087007929 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 159087007930 ATP binding site [chemical binding]; other site 159087007931 G-X-G motif; other site 159087007932 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087007933 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 159087007934 active site 159087007935 phosphorylation site [posttranslational modification] 159087007936 intermolecular recognition site; other site 159087007937 dimerization interface [polypeptide binding]; other site 159087007938 putative carbohydrate kinase; Provisional; Region: PRK10565 159087007939 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 159087007940 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 159087007941 putative substrate binding site [chemical binding]; other site 159087007942 putative ATP binding site [chemical binding]; other site 159087007943 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 159087007944 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 159087007945 dimerization interface [polypeptide binding]; other site 159087007946 active site 159087007947 Methyltransferase domain; Region: Methyltransf_23; pfam13489 159087007948 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 159087007949 S-adenosylmethionine binding site [chemical binding]; other site 159087007950 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 159087007951 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 159087007952 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087007953 catalytic residue [active] 159087007954 Uncharacterized conserved protein (DUF2249); Region: DUF2249; pfam10006 159087007955 Rhomboid family; Region: Rhomboid; pfam01694 159087007956 homoserine dehydrogenase; Provisional; Region: PRK06349 159087007957 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 159087007958 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 159087007959 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 159087007960 aminotransferase AlaT; Validated; Region: PRK09265 159087007961 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 159087007962 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087007963 homodimer interface [polypeptide binding]; other site 159087007964 catalytic residue [active] 159087007965 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 159087007966 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 159087007967 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 159087007968 Substrate binding site; other site 159087007969 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 159087007970 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087007971 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 159087007972 Walker A/P-loop; other site 159087007973 ATP binding site [chemical binding]; other site 159087007974 Q-loop/lid; other site 159087007975 ABC transporter signature motif; other site 159087007976 Walker B; other site 159087007977 D-loop; other site 159087007978 H-loop/switch region; other site 159087007979 PEP-CTERM motif; Region: VPEP; pfam07589 159087007980 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 159087007981 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087007982 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087007983 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 159087007984 FtsX-like permease family; Region: FtsX; pfam02687 159087007985 hypothetical protein; Validated; Region: PRK08223 159087007986 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 159087007987 ATP binding site [chemical binding]; other site 159087007988 substrate interface [chemical binding]; other site 159087007989 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 159087007990 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 159087007991 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 159087007992 Chain length determinant protein; Region: Wzz; cl15801 159087007993 exopolysaccharide/PEP-CTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 159087007994 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 159087007995 uncharacterized protein, PEP-CTERM system associated; Region: pepcterm_hypo_1; TIGR03016 159087007996 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 159087007997 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 159087007998 Walker A motif; other site 159087007999 ATP binding site [chemical binding]; other site 159087008000 Walker B motif; other site 159087008001 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 159087008002 active site 159087008003 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 159087008004 homodimer interface [polypeptide binding]; other site 159087008005 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); Region: CE4_PuuE_HpPgdA_like_2; cd10941 159087008006 polysaccharide deacetylase family protein, PEP-CTERM locus subfamily; Region: pepcterm_polyde; TIGR03006 159087008007 putative active site [active] 159087008008 putative catalytic site [active] 159087008009 FemAB-related protein, PEP-CTERM system-associated; Region: pepcterm_femAB; TIGR03019 159087008010 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 159087008011 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 159087008012 exosortase A; Region: exosortase_1; TIGR03109 159087008013 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 159087008014 EpsI family protein; Region: EpsI_fam; TIGR02914 159087008015 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 159087008016 This family is most closely related to the GT1 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis; Region: GT1_WbnK_like; cd03807 159087008017 putative ADP-binding pocket [chemical binding]; other site 159087008018 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 159087008019 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 159087008020 active site 159087008021 dimer interface [polypeptide binding]; other site 159087008022 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 159087008023 Ligand Binding Site [chemical binding]; other site 159087008024 Molecular Tunnel; other site 159087008025 PEP-CTERM/exosortase A-associated glycosyltransferase, Daro_2409 family; Region: stp3; TIGR04063 159087008026 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 159087008027 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 159087008028 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087008029 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087008030 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 159087008031 acyl-activating enzyme (AAE) consensus motif; other site 159087008032 active site 159087008033 AMP binding site [chemical binding]; other site 159087008034 CoA binding site [chemical binding]; other site 159087008035 probable O-glycosylation ligase, exosortase A-associated; Region: PEP_O_lig_1; TIGR03097 159087008036 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 159087008037 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 159087008038 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 159087008039 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 159087008040 active site 159087008041 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 159087008042 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087008043 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 159087008044 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 159087008045 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 159087008046 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 159087008047 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087008048 Acyltransferase family; Region: Acyl_transf_3; pfam01757 159087008049 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 159087008050 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 159087008051 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 159087008052 TPR motif; other site 159087008053 TPR repeat; Region: TPR_11; pfam13414 159087008054 binding surface 159087008055 Transposase; Region: HTH_Tnp_1; pfam01527 159087008056 HTH-like domain; Region: HTH_21; pfam13276 159087008057 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 159087008058 Integrase core domain; Region: rve; pfam00665 159087008059 Integrase core domain; Region: rve_3; pfam13683 159087008060 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 159087008061 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 159087008062 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 159087008063 Ligand Binding Site [chemical binding]; other site 159087008064 Molecular Tunnel; other site 159087008065 VanZ like family; Region: VanZ; cl01971 159087008066 VanZ like family; Region: VanZ; cl01971 159087008067 exosortase A system-associated hydrolase 1; Region: hydr1_PEP; TIGR03100 159087008068 exosortase A system-associated hydrolase 2; Region: hydr2_PEP; TIGR03101 159087008069 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 159087008070 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 159087008071 acyl-CoA ligase (AMP-forming), exosortase A-associated; Region: ligase_PEP_1; TIGR03098 159087008072 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087008073 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_6; cd05922 159087008074 acyl-activating enzyme (AAE) consensus motif; other site 159087008075 acyl-activating enzyme (AAE) consensus motif; other site 159087008076 putative AMP binding site [chemical binding]; other site 159087008077 putative active site [active] 159087008078 putative CoA binding site [chemical binding]; other site 159087008079 pyridoxal-dependent decarboxylase, exosortase A system-associated; Region: dCO2ase_PEP1; TIGR03099 159087008080 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase; Region: PLPDE_III_Btrk_like; cd06839 159087008081 dimer interface [polypeptide binding]; other site 159087008082 active site 159087008083 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087008084 catalytic residues [active] 159087008085 substrate binding site [chemical binding]; other site 159087008086 sugar transferase, PEP-CTERM system associated; Region: EpsB_2; TIGR03013 159087008087 Bacterial sugar transferase; Region: Bac_transf; pfam02397 159087008088 putative PEP-CTERM system histidine kinase; Region: PEP_his_kin; TIGR02916 159087008089 GAF domain; Region: GAF_3; pfam13492 159087008090 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 159087008091 dimer interface [polypeptide binding]; other site 159087008092 phosphorylation site [posttranslational modification] 159087008093 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 159087008094 ATP binding site [chemical binding]; other site 159087008095 Mg2+ binding site [ion binding]; other site 159087008096 G-X-G motif; other site 159087008097 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 159087008098 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 159087008099 active site 159087008100 phosphorylation site [posttranslational modification] 159087008101 intermolecular recognition site; other site 159087008102 dimerization interface [polypeptide binding]; other site 159087008103 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 159087008104 Walker A motif; other site 159087008105 ATP binding site [chemical binding]; other site 159087008106 Walker B motif; other site 159087008107 arginine finger; other site 159087008108 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 159087008109 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 159087008110 binding surface 159087008111 TPR motif; other site 159087008112 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 159087008113 binding surface 159087008114 TPR motif; other site 159087008115 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 159087008116 binding surface 159087008117 TPR motif; other site 159087008118 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 159087008119 binding surface 159087008120 TPR motif; other site 159087008121 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 159087008122 binding surface 159087008123 TPR motif; other site 159087008124 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 159087008125 binding surface 159087008126 TPR motif; other site 159087008127 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 159087008128 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 159087008129 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 159087008130 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 159087008131 Sel1 repeat; Region: Sel1; cl02723 159087008132 Sel1-like repeats; Region: SEL1; smart00671 159087008133 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 159087008134 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 159087008135 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087008136 catalytic residue [active] 159087008137 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 159087008138 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 159087008139 PqqD family protein, HPr-rel-A system; Region: PqqD_rel_X; TIGR04353 159087008140 HprK-related kinase A; Region: HprK_rel_A; TIGR04352 159087008141 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 159087008142 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 159087008143 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 159087008144 RNase E interface [polypeptide binding]; other site 159087008145 trimer interface [polypeptide binding]; other site 159087008146 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 159087008147 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 159087008148 RNase E interface [polypeptide binding]; other site 159087008149 trimer interface [polypeptide binding]; other site 159087008150 active site 159087008151 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 159087008152 putative nucleic acid binding region [nucleotide binding]; other site 159087008153 G-X-X-G motif; other site 159087008154 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 159087008155 RNA binding site [nucleotide binding]; other site 159087008156 domain interface; other site 159087008157 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 159087008158 16S/18S rRNA binding site [nucleotide binding]; other site 159087008159 S13e-L30e interaction site [polypeptide binding]; other site 159087008160 25S rRNA binding site [nucleotide binding]; other site 159087008161 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 159087008162 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 159087008163 RNA binding site [nucleotide binding]; other site 159087008164 active site 159087008165 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 159087008166 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 159087008167 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 159087008168 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 159087008169 translation initiation factor IF-2; Region: IF-2; TIGR00487 159087008170 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 159087008171 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 159087008172 G1 box; other site 159087008173 putative GEF interaction site [polypeptide binding]; other site 159087008174 GTP/Mg2+ binding site [chemical binding]; other site 159087008175 Switch I region; other site 159087008176 G2 box; other site 159087008177 G3 box; other site 159087008178 Switch II region; other site 159087008179 G4 box; other site 159087008180 G5 box; other site 159087008181 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 159087008182 Translation-initiation factor 2; Region: IF-2; pfam11987 159087008183 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 159087008184 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 159087008185 NusA N-terminal domain; Region: NusA_N; pfam08529 159087008186 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 159087008187 RNA binding site [nucleotide binding]; other site 159087008188 homodimer interface [polypeptide binding]; other site 159087008189 NusA-like KH domain; Region: KH_5; pfam13184 159087008190 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 159087008191 G-X-X-G motif; other site 159087008192 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 159087008193 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 159087008194 ribosome maturation protein RimP; Reviewed; Region: PRK00092 159087008195 Sm and related proteins; Region: Sm_like; cl00259 159087008196 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 159087008197 putative oligomer interface [polypeptide binding]; other site 159087008198 putative RNA binding site [nucleotide binding]; other site 159087008199 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 159087008200 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 159087008201 RNA binding surface [nucleotide binding]; other site 159087008202 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 159087008203 probable active site [active] 159087008204 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 159087008205 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 159087008206 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 159087008207 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 159087008208 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 159087008209 active site 159087008210 HIGH motif; other site 159087008211 dimer interface [polypeptide binding]; other site 159087008212 KMSKS motif; other site 159087008213 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 159087008214 Peptidase family M50; Region: Peptidase_M50; pfam02163 159087008215 active site 159087008216 putative substrate binding region [chemical binding]; other site 159087008217 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 159087008218 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 159087008219 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 159087008220 active site 159087008221 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 159087008222 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 159087008223 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 159087008224 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 159087008225 lipoyl attachment site [posttranslational modification]; other site 159087008226 glycine dehydrogenase; Provisional; Region: PRK05367 159087008227 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 159087008228 tetramer interface [polypeptide binding]; other site 159087008229 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087008230 catalytic residue [active] 159087008231 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 159087008232 tetramer interface [polypeptide binding]; other site 159087008233 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087008234 catalytic residue [active] 159087008235 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 159087008236 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 159087008237 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 159087008238 HSP70 interaction site [polypeptide binding]; other site 159087008239 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 159087008240 substrate binding site [polypeptide binding]; other site 159087008241 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 159087008242 Zn binding sites [ion binding]; other site 159087008243 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 159087008244 dimer interface [polypeptide binding]; other site 159087008245 Arginase family; Region: Arginase; cd09989 159087008246 active site 159087008247 Mn binding site [ion binding]; other site 159087008248 oligomer interface [polypeptide binding]; other site 159087008249 Protein of unknown function, DUF480; Region: DUF480; pfam04337 159087008250 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 159087008251 catalytic site [active] 159087008252 putative active site [active] 159087008253 putative substrate binding site [chemical binding]; other site 159087008254 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 159087008255 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 159087008256 GIY-YIG motif/motif A; other site 159087008257 putative active site [active] 159087008258 putative metal binding site [ion binding]; other site 159087008259 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 159087008260 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 159087008261 dimerization interface [polypeptide binding]; other site 159087008262 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 159087008263 dimer interface [polypeptide binding]; other site 159087008264 phosphorylation site [posttranslational modification] 159087008265 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 159087008266 ATP binding site [chemical binding]; other site 159087008267 Mg2+ binding site [ion binding]; other site 159087008268 G-X-G motif; other site 159087008269 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 159087008270 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 159087008271 active site 159087008272 phosphorylation site [posttranslational modification] 159087008273 intermolecular recognition site; other site 159087008274 dimerization interface [polypeptide binding]; other site 159087008275 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 159087008276 DNA binding site [nucleotide binding] 159087008277 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; pfam01062 159087008278 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 159087008279 Outer membrane efflux protein; Region: OEP; pfam02321 159087008280 Outer membrane efflux protein; Region: OEP; pfam02321 159087008281 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 159087008282 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087008283 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 159087008284 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087008285 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 159087008286 active site 159087008287 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 159087008288 phosphate binding protein; Region: ptsS_2; TIGR02136 159087008289 Transposase domain (DUF772); Region: DUF772; pfam05598 159087008290 ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PhnD; COG3221 159087008291 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 159087008292 dimer interface [polypeptide binding]; other site 159087008293 phosphorylation site [posttranslational modification] 159087008294 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 159087008295 ATP binding site [chemical binding]; other site 159087008296 Mg2+ binding site [ion binding]; other site 159087008297 G-X-G motif; other site 159087008298 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087008299 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 159087008300 active site 159087008301 phosphorylation site [posttranslational modification] 159087008302 intermolecular recognition site; other site 159087008303 dimerization interface [polypeptide binding]; other site 159087008304 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 159087008305 DNA binding residues [nucleotide binding] 159087008306 dimerization interface [polypeptide binding]; other site 159087008307 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087008308 Cytochrome c; Region: Cytochrom_C; pfam00034 159087008309 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087008310 Cytochrome c [Energy production and conversion]; Region: COG3258 159087008311 Cytochrome c; Region: Cytochrom_C; pfam00034 159087008312 DsrE/DsrF-like family; Region: DrsE; pfam02635 159087008313 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 159087008314 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087008315 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 159087008316 putative dimerization interface [polypeptide binding]; other site 159087008317 Predicted membrane protein [Function unknown]; Region: COG2855 159087008318 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087008319 dimer interface [polypeptide binding]; other site 159087008320 putative CheW interface [polypeptide binding]; other site 159087008321 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 159087008322 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 159087008323 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 159087008324 active site 159087008325 Int/Topo IB signature motif; other site 159087008326 catalytic residues [active] 159087008327 DNA binding site [nucleotide binding] 159087008328 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 159087008329 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 159087008330 catalytic residues [active] 159087008331 catalytic nucleophile [active] 159087008332 bZIP Maf transcription factor; Region: bZIP_Maf; pfam03131 159087008333 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 159087008334 BRO family, N-terminal domain; Region: Bro-N; cl10591 159087008335 KilA-N domain; Region: KilA-N; pfam04383 159087008336 Protein of unknown function (DUF1353); Region: DUF1353; pfam07087 159087008337 Prophage antirepressor [Transcription]; Region: COG3617 159087008338 BRO family, N-terminal domain; Region: Bro-N; smart01040 159087008339 aspartate kinase; Reviewed; Region: PRK06635 159087008340 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 159087008341 putative nucleotide binding site [chemical binding]; other site 159087008342 putative catalytic residues [active] 159087008343 putative Mg ion binding site [ion binding]; other site 159087008344 putative aspartate binding site [chemical binding]; other site 159087008345 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 159087008346 putative allosteric regulatory site; other site 159087008347 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 159087008348 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 159087008349 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 159087008350 putative active site [active] 159087008351 Zn binding site [ion binding]; other site 159087008352 MoxR-like ATPases [General function prediction only]; Region: COG0714 159087008353 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 159087008354 Walker A motif; other site 159087008355 ATP binding site [chemical binding]; other site 159087008356 Walker B motif; other site 159087008357 arginine finger; other site 159087008358 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 159087008359 Protein of unknown function DUF58; Region: DUF58; pfam01882 159087008360 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 159087008361 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 159087008362 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 159087008363 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 159087008364 Transglycosylase SLT domain; Region: SLT_2; pfam13406 159087008365 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 159087008366 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087008367 catalytic residue [active] 159087008368 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 159087008369 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 159087008370 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087008371 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 159087008372 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 159087008373 DNA binding residues [nucleotide binding] 159087008374 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 159087008375 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 159087008376 Peptidase family M23; Region: Peptidase_M23; pfam01551 159087008377 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 159087008378 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 159087008379 S-adenosylmethionine binding site [chemical binding]; other site 159087008380 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 159087008381 H-NS histone family; Region: Histone_HNS; pfam00816 159087008382 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 159087008383 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 159087008384 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 159087008385 active site 159087008386 Int/Topo IB signature motif; other site 159087008387 PRTRC system protein D; Region: PRTRC_D; TIGR03739 159087008388 Plasmid segregation protein ParM and similar proteins; Region: ParM_like; cd10227 159087008389 Mg binding site [ion binding]; other site 159087008390 nucleotide binding site [chemical binding]; other site 159087008391 putative protofilament interface [polypeptide binding]; other site 159087008392 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 159087008393 Integrase; Region: Integrase_1; pfam12835 159087008394 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 159087008395 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 159087008396 oligomeric interface; other site 159087008397 putative active site [active] 159087008398 homodimer interface [polypeptide binding]; other site 159087008399 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 159087008400 PRTRC system ThiF family protein; Region: PRTRC_ThiF; TIGR03736 159087008401 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cl17196 159087008402 ATP binding site [chemical binding]; other site 159087008403 substrate interface [chemical binding]; other site 159087008404 Domain of unknown function (DUF2016); Region: DUF2016; pfam09436 159087008405 PRTRC system protein A; Region: PRTRC_A; TIGR03735 159087008406 Prokaryotic homologs of the JAB domain; Region: Prok-JAB; pfam14464 159087008407 Prokaryotic E2 family D; Region: Prok-E2_D; cl14019 159087008408 PRTRC system protein F; Region: PRTRC_F; TIGR03742 159087008409 Alpha-helical domain 2; Region: alpha-hel2; pfam14456 159087008410 PRTRC system protein C; Region: PRTRC_C; TIGR03738 159087008411 PRTRC system protein E; Region: PRTRC_E; TIGR03741 159087008412 ParB-like nuclease domain; Region: ParB; smart00470 159087008413 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 159087008414 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 159087008415 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 159087008416 S-adenosylmethionine binding site [chemical binding]; other site 159087008417 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 159087008418 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 159087008419 DEAD-like helicases superfamily; Region: DEXDc; smart00487 159087008420 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 159087008421 helicase superfamily c-terminal domain; Region: HELICc; smart00490 159087008422 Caspase domain; Region: Peptidase_C14; pfam00656 159087008423 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 159087008424 MPN+ (JAMM) motif; other site 159087008425 Zinc-binding site [ion binding]; other site 159087008426 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 159087008427 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087008428 Walker A/P-loop; other site 159087008429 ATP binding site [chemical binding]; other site 159087008430 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087008431 AAA domain; Region: AAA_21; pfam13304 159087008432 Walker A/P-loop; other site 159087008433 ATP binding site [chemical binding]; other site 159087008434 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 159087008435 putative active site [active] 159087008436 putative metal-binding site [ion binding]; other site 159087008437 Part of AAA domain; Region: AAA_19; pfam13245 159087008438 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 159087008439 Family description; Region: UvrD_C_2; pfam13538 159087008440 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 159087008441 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 159087008442 active site 159087008443 metal binding site [ion binding]; metal-binding site 159087008444 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 159087008445 IHF dimer interface [polypeptide binding]; other site 159087008446 IHF - DNA interface [nucleotide binding]; other site 159087008447 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 159087008448 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 159087008449 active site 159087008450 catalytic residues [active] 159087008451 Int/Topo IB signature motif; other site 159087008452 DNA binding site [nucleotide binding] 159087008453 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 159087008454 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 159087008455 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 159087008456 salt bridge; other site 159087008457 non-specific DNA binding site [nucleotide binding]; other site 159087008458 sequence-specific DNA binding site [nucleotide binding]; other site 159087008459 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 159087008460 Zinc-binding domain of primase-helicase; Region: Prim_Zn_Ribbon; smart00778 159087008461 CHC2 zinc finger; Region: zf-CHC2; cl17510 159087008462 Toprim domain; Region: Toprim_3; pfam13362 159087008463 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 159087008464 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 159087008465 FeS/SAM binding site; other site 159087008466 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 159087008467 Ethylbenzene dehydrogenase; Region: EB_dh; smart00887 159087008468 putative ligand binding site [chemical binding]; other site 159087008469 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 159087008470 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 159087008471 Chlorite dismutase; Region: Chlor_dismutase; pfam06778 159087008472 DMSO reductase family type II enzyme chaperone; Region: DMSO_red_II_cha; TIGR03482 159087008473 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 159087008474 DMSO reductase family type II enzyme, iron-sulfur subunit; Region: DMSO_red_II_bet; TIGR03478 159087008475 DMSO reductase family type II enzyme, molybdopterin subunit; Region: DMSO_red_II_alp; TIGR03479 159087008476 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 159087008477 [4Fe-4S] binding site [ion binding]; other site 159087008478 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 159087008479 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 159087008480 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 159087008481 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 159087008482 molybdopterin cofactor binding site; other site 159087008483 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087008484 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 159087008485 active site 159087008486 phosphorylation site [posttranslational modification] 159087008487 intermolecular recognition site; other site 159087008488 dimerization interface [polypeptide binding]; other site 159087008489 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 159087008490 Walker A motif; other site 159087008491 ATP binding site [chemical binding]; other site 159087008492 Walker B motif; other site 159087008493 arginine finger; other site 159087008494 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087008495 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087008496 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 159087008497 dimerization interface [polypeptide binding]; other site 159087008498 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 159087008499 dimer interface [polypeptide binding]; other site 159087008500 phosphorylation site [posttranslational modification] 159087008501 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 159087008502 ATP binding site [chemical binding]; other site 159087008503 Mg2+ binding site [ion binding]; other site 159087008504 G-X-G motif; other site 159087008505 PAS fold; Region: PAS_4; pfam08448 159087008506 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 159087008507 putative active site [active] 159087008508 heme pocket [chemical binding]; other site 159087008509 PAS domain S-box; Region: sensory_box; TIGR00229 159087008510 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 159087008511 putative active site [active] 159087008512 heme pocket [chemical binding]; other site 159087008513 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 159087008514 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 159087008515 RNA polymerase sigma factor; Provisional; Region: PRK12536 159087008516 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 159087008517 DNA binding residues [nucleotide binding] 159087008518 Thiosulfate reductase cytochrome B subunit (membrane anchoring protein) [Energy production and conversion]; Region: COG4117 159087008519 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 159087008520 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 159087008521 bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they...; Region: bact_SO_family_Moco; cd02108 159087008522 Moco binding site; other site 159087008523 metal coordination site [ion binding]; other site 159087008524 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 159087008525 Putative helicase; Region: TraI_2; pfam07514 159087008526 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 159087008527 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 159087008528 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 159087008529 Domain of unknown function (DUF4400); Region: DUF4400; cl14023 159087008530 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087008531 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 159087008532 active site 159087008533 phosphorylation site [posttranslational modification] 159087008534 intermolecular recognition site; other site 159087008535 dimerization interface [polypeptide binding]; other site 159087008536 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 159087008537 Walker A motif; other site 159087008538 ATP binding site [chemical binding]; other site 159087008539 Walker B motif; other site 159087008540 arginine finger; other site 159087008541 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087008542 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 159087008543 dimerization interface [polypeptide binding]; other site 159087008544 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 159087008545 dimer interface [polypeptide binding]; other site 159087008546 phosphorylation site [posttranslational modification] 159087008547 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 159087008548 ATP binding site [chemical binding]; other site 159087008549 G-X-G motif; other site 159087008550 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087008551 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 159087008552 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 159087008553 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 159087008554 tetrathionate reductase subunit C; Provisional; Region: PRK14992 159087008555 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 159087008556 This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_Arsenate-R; cd02757 159087008557 putative [Fe4-S4] binding site [ion binding]; other site 159087008558 putative molybdopterin cofactor binding site [chemical binding]; other site 159087008559 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 159087008560 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 159087008561 putative molybdopterin cofactor binding site; other site 159087008562 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 159087008563 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 159087008564 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 159087008565 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087008566 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087008567 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 159087008568 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 159087008569 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 159087008570 FeS/SAM binding site; other site 159087008571 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 159087008572 Domain of unknown function (DUF2703); Region: DUF2703; pfam10865 159087008573 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 159087008574 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087008575 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087008576 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 159087008577 Protein of unknown function, DUF; Region: DUF411; cl01142 159087008578 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 159087008579 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 159087008580 Nitrogen regulatory protein P-II; Region: P-II; cl00412 159087008581 Nitrogen regulatory protein P-II; Region: P-II; smart00938 159087008582 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087008583 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087008584 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087008585 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087008586 Outer membrane efflux protein; Region: OEP; pfam02321 159087008587 Outer membrane efflux protein; Region: OEP; pfam02321 159087008588 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 159087008589 lipoprotein signal peptidase; Provisional; Region: PRK14787 159087008590 Heavy-metal-associated domain; Region: HMA; pfam00403 159087008591 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 159087008592 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087008593 Soluble P-type ATPase [General function prediction only]; Region: COG4087 159087008594 hypothetical protein; Provisional; Region: PRK02237 159087008595 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 159087008596 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 159087008597 DNA binding residues [nucleotide binding] 159087008598 dimer interface [polypeptide binding]; other site 159087008599 putative metal binding site [ion binding]; other site 159087008600 RNA polymerase sigma factor, SigZ family; Region: SigZ; TIGR02959 159087008601 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087008602 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 159087008603 DNA binding residues [nucleotide binding] 159087008604 OsmC-like protein; Region: OsmC; pfam02566 159087008605 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 159087008606 arsenical-resistance protein; Region: acr3; TIGR00832 159087008607 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 159087008608 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 159087008609 P loop; other site 159087008610 Nucleotide binding site [chemical binding]; other site 159087008611 DTAP/Switch II; other site 159087008612 Switch I; other site 159087008613 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 159087008614 DTAP/Switch II; other site 159087008615 Switch I; other site 159087008616 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 159087008617 Low molecular weight phosphatase family; Region: LMWPc; cl00105 159087008618 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 159087008619 Low molecular weight phosphatase family; Region: LMWPc; cd00115 159087008620 active site 159087008621 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 159087008622 putative DNA binding site [nucleotide binding]; other site 159087008623 putative Zn2+ binding site [ion binding]; other site 159087008624 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 159087008625 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 159087008626 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087008627 catalytic residue [active] 159087008628 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087008629 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087008630 ligand binding site [chemical binding]; other site 159087008631 TraL protein; Region: TraL; pfam07178 159087008632 type IV conjugative transfer system protein TraE; Region: TraE_TIGR; TIGR02761 159087008633 TraK protein; Region: TraK; pfam06586 159087008634 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 159087008635 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 159087008636 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 159087008637 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 159087008638 dimerization domain [polypeptide binding]; other site 159087008639 dimer interface [polypeptide binding]; other site 159087008640 catalytic residues [active] 159087008641 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 159087008642 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 159087008643 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 159087008644 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 159087008645 Walker A motif; other site 159087008646 ATP binding site [chemical binding]; other site 159087008647 conjugative transfer signal peptidase TraF; Region: TraF_Ti; TIGR02771 159087008648 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 159087008649 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 159087008650 TraU protein; Region: TraU; pfam06834 159087008651 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; pfam09673 159087008652 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 159087008653 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 159087008654 TraF-like protein; Region: TraF-like; TIGR02740 159087008655 F plasmid transfer operon protein; Region: TraF; pfam13728 159087008656 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 159087008657 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 159087008658 Fic/DOC family; Region: Fic; pfam02661 159087008659 AAA domain; Region: AAA_23; pfam13476 159087008660 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 159087008661 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 159087008662 DNA binding residues [nucleotide binding] 159087008663 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 159087008664 IHF - DNA interface [nucleotide binding]; other site 159087008665 IHF dimer interface [polypeptide binding]; other site 159087008666 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 159087008667 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 159087008668 putative tRNA-binding site [nucleotide binding]; other site 159087008669 B3/4 domain; Region: B3_4; pfam03483 159087008670 tRNA synthetase B5 domain; Region: B5; smart00874 159087008671 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 159087008672 dimer interface [polypeptide binding]; other site 159087008673 motif 1; other site 159087008674 motif 3; other site 159087008675 motif 2; other site 159087008676 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 159087008677 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 159087008678 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 159087008679 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 159087008680 dimer interface [polypeptide binding]; other site 159087008681 motif 1; other site 159087008682 active site 159087008683 motif 2; other site 159087008684 motif 3; other site 159087008685 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 159087008686 23S rRNA binding site [nucleotide binding]; other site 159087008687 L21 binding site [polypeptide binding]; other site 159087008688 L13 binding site [polypeptide binding]; other site 159087008689 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 159087008690 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 159087008691 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 159087008692 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 159087008693 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 159087008694 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 159087008695 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 159087008696 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 159087008697 active site 159087008698 dimer interface [polypeptide binding]; other site 159087008699 motif 1; other site 159087008700 motif 2; other site 159087008701 motif 3; other site 159087008702 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 159087008703 anticodon binding site; other site 159087008704 SlyX; Region: SlyX; pfam04102 159087008705 DHHA1 domain; Region: DHHA1; pfam02272 159087008706 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087008707 Hemerythrin; Region: Hemerythrin; cd12107 159087008708 Fe binding site [ion binding]; other site 159087008709 PEP-CTERM motif; Region: VPEP; pfam07589 159087008710 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 159087008711 Zinc-binding domain of primase-helicase; Region: Prim_Zn_Ribbon; smart00778 159087008712 CHC2 zinc finger; Region: zf-CHC2; cl17510 159087008713 Toprim domain; Region: Toprim_3; pfam13362 159087008714 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 159087008715 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 159087008716 ATP binding site [chemical binding]; other site 159087008717 putative Mg++ binding site [ion binding]; other site 159087008718 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 159087008719 nucleotide binding region [chemical binding]; other site 159087008720 ATP-binding site [chemical binding]; other site 159087008721 Protein of unknown function (DUF1376); Region: DUF1376; pfam07120 159087008722 Helix-turn-helix domain; Region: HTH_39; pfam14090 159087008723 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 159087008724 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 159087008725 integrase; Provisional; Region: PRK09692 159087008726 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 159087008727 active site 159087008728 Int/Topo IB signature motif; other site 159087008729 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 159087008730 active site lid residues [active] 159087008731 substrate binding pocket [chemical binding]; other site 159087008732 catalytic residues [active] 159087008733 substrate-Mg2+ binding site; other site 159087008734 aspartate-rich region 1; other site 159087008735 aspartate-rich region 2; other site 159087008736 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 159087008737 active site lid residues [active] 159087008738 substrate binding pocket [chemical binding]; other site 159087008739 catalytic residues [active] 159087008740 substrate-Mg2+ binding site; other site 159087008741 aspartate-rich region 1; other site 159087008742 aspartate-rich region 2; other site 159087008743 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 159087008744 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 159087008745 acetyl-CoA synthetase; Provisional; Region: PRK04319 159087008746 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 159087008747 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087008748 acyl-activating enzyme (AAE) consensus motif; other site 159087008749 AMP binding site [chemical binding]; other site 159087008750 active site 159087008751 CoA binding site [chemical binding]; other site 159087008752 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 159087008753 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 159087008754 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 159087008755 Coenzyme A binding pocket [chemical binding]; other site 159087008756 TonB C terminal; Region: TonB_2; pfam13103 159087008757 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087008758 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_2; cd06335 159087008759 putative ligand binding site [chemical binding]; other site 159087008760 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 159087008761 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 159087008762 Walker A/P-loop; other site 159087008763 ATP binding site [chemical binding]; other site 159087008764 Q-loop/lid; other site 159087008765 ABC transporter signature motif; other site 159087008766 Walker B; other site 159087008767 D-loop; other site 159087008768 H-loop/switch region; other site 159087008769 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 159087008770 active site 159087008771 catalytic triad [active] 159087008772 oxyanion hole [active] 159087008773 switch loop; other site 159087008774 tRNA 2-selenouridine synthase; Region: tRNA_sel_U_synt; TIGR03167 159087008775 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 159087008776 active site residue [active] 159087008777 Methyltransferase domain; Region: Methyltransf_23; pfam13489 159087008778 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 159087008779 S-adenosylmethionine binding site [chemical binding]; other site 159087008780 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 159087008781 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 159087008782 CoA binding domain; Region: CoA_binding_2; pfam13380 159087008783 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 159087008784 CoA-ligase; Region: Ligase_CoA; pfam00549 159087008785 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 159087008786 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 159087008787 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087008788 Coenzyme A binding pocket [chemical binding]; other site 159087008789 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 159087008790 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 159087008791 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 159087008792 HflX GTPase family; Region: HflX; cd01878 159087008793 G1 box; other site 159087008794 GTP/Mg2+ binding site [chemical binding]; other site 159087008795 Switch I region; other site 159087008796 G2 box; other site 159087008797 G3 box; other site 159087008798 Switch II region; other site 159087008799 G4 box; other site 159087008800 G5 box; other site 159087008801 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 159087008802 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 159087008803 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 159087008804 NAD(P) binding site [chemical binding]; other site 159087008805 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 159087008806 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087008807 catalytic residue [active] 159087008808 Protein of unknown function (DUF1684); Region: DUF1684; pfam07920 159087008809 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_1; cd08894 159087008810 putative hydrophobic ligand binding site [chemical binding]; other site 159087008811 Protein of unknown function (DUF2502); Region: DUF2502; pfam10697 159087008812 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 159087008813 Clp amino terminal domain; Region: Clp_N; pfam02861 159087008814 Clp amino terminal domain; Region: Clp_N; pfam02861 159087008815 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 159087008816 Walker A motif; other site 159087008817 ATP binding site [chemical binding]; other site 159087008818 Walker B motif; other site 159087008819 arginine finger; other site 159087008820 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 159087008821 Walker A motif; other site 159087008822 ATP binding site [chemical binding]; other site 159087008823 Walker B motif; other site 159087008824 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 159087008825 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 159087008826 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 159087008827 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087008828 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087008829 dimer interface [polypeptide binding]; other site 159087008830 putative CheW interface [polypeptide binding]; other site 159087008831 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 159087008832 MoaE homodimer interface [polypeptide binding]; other site 159087008833 MoaD interaction [polypeptide binding]; other site 159087008834 active site residues [active] 159087008835 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 159087008836 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 159087008837 G1 box; other site 159087008838 putative GEF interaction site [polypeptide binding]; other site 159087008839 GTP/Mg2+ binding site [chemical binding]; other site 159087008840 Switch I region; other site 159087008841 G2 box; other site 159087008842 G3 box; other site 159087008843 Switch II region; other site 159087008844 G4 box; other site 159087008845 G5 box; other site 159087008846 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 159087008847 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 159087008848 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 159087008849 active site 159087008850 phosphate binding residues; other site 159087008851 catalytic residues [active] 159087008852 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 159087008853 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 159087008854 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 159087008855 homodimer interface [polypeptide binding]; other site 159087008856 chemical substrate binding site [chemical binding]; other site 159087008857 oligomer interface [polypeptide binding]; other site 159087008858 metal binding site [ion binding]; metal-binding site 159087008859 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 159087008860 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 159087008861 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 159087008862 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 159087008863 trimer interface [polypeptide binding]; other site 159087008864 putative metal binding site [ion binding]; other site 159087008865 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 159087008866 A new structural DNA glycosylase containing HEAT-like repeats; Region: AlkD_like_1; cd07064 159087008867 active site 159087008868 flagellar assembly protein FliW; Provisional; Region: PRK13284 159087008869 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 159087008870 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 159087008871 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 159087008872 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 159087008873 RNA binding site [nucleotide binding]; other site 159087008874 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 159087008875 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 159087008876 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 159087008877 FAD binding pocket [chemical binding]; other site 159087008878 FAD binding motif [chemical binding]; other site 159087008879 phosphate binding motif [ion binding]; other site 159087008880 beta-alpha-beta structure motif; other site 159087008881 NAD binding pocket [chemical binding]; other site 159087008882 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 159087008883 ArsC family; Region: ArsC; pfam03960 159087008884 putative catalytic residues [active] 159087008885 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 159087008886 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 159087008887 dimerization interface [polypeptide binding]; other site 159087008888 domain crossover interface; other site 159087008889 redox-dependent activation switch; other site 159087008890 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087008891 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 159087008892 dimer interface [polypeptide binding]; other site 159087008893 phosphorylation site [posttranslational modification] 159087008894 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 159087008895 ATP binding site [chemical binding]; other site 159087008896 Mg2+ binding site [ion binding]; other site 159087008897 G-X-G motif; other site 159087008898 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087008899 FAD binding domain; Region: FAD_binding_4; pfam01565 159087008900 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 159087008901 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 159087008902 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 159087008903 FeS/SAM binding site; other site 159087008904 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 159087008905 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087008906 Zn2+ binding site [ion binding]; other site 159087008907 Mg2+ binding site [ion binding]; other site 159087008908 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 159087008909 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 159087008910 PAS domain; Region: PAS_9; pfam13426 159087008911 putative active site [active] 159087008912 heme pocket [chemical binding]; other site 159087008913 PAS fold; Region: PAS_7; pfam12860 159087008914 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087008915 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 159087008916 putative active site [active] 159087008917 heme pocket [chemical binding]; other site 159087008918 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 159087008919 dimer interface [polypeptide binding]; other site 159087008920 phosphorylation site [posttranslational modification] 159087008921 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 159087008922 ATP binding site [chemical binding]; other site 159087008923 Mg2+ binding site [ion binding]; other site 159087008924 G-X-G motif; other site 159087008925 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 159087008926 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008927 active site 159087008928 phosphorylation site [posttranslational modification] 159087008929 intermolecular recognition site; other site 159087008930 dimerization interface [polypeptide binding]; other site 159087008931 Response regulator receiver domain; Region: Response_reg; pfam00072 159087008932 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 159087008933 active site 159087008934 phosphorylation site [posttranslational modification] 159087008935 intermolecular recognition site; other site 159087008936 dimerization interface [polypeptide binding]; other site 159087008937 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 159087008938 Mechanosensitive ion channel; Region: MS_channel; pfam00924 159087008939 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 159087008940 putative active site [active] 159087008941 YdjC motif; other site 159087008942 Mg binding site [ion binding]; other site 159087008943 putative homodimer interface [polypeptide binding]; other site 159087008944 GtrA-like protein; Region: GtrA; pfam04138 159087008945 Predicted membrane protein [Function unknown]; Region: COG2246 159087008946 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 159087008947 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 159087008948 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 159087008949 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 159087008950 Ligand binding site; other site 159087008951 Putative Catalytic site; other site 159087008952 DXD motif; other site 159087008953 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 159087008954 benzoate transporter; Region: benE; TIGR00843 159087008955 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 159087008956 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 159087008957 active site 159087008958 catalytic tetrad [active] 159087008959 Hemerythrin; Region: Hemerythrin; cd12107 159087008960 Fe binding site [ion binding]; other site 159087008961 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087008962 dimer interface [polypeptide binding]; other site 159087008963 putative CheW interface [polypeptide binding]; other site 159087008964 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 159087008965 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087008966 putative ligand binding site [chemical binding]; other site 159087008967 EamA-like transporter family; Region: EamA; pfam00892 159087008968 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 159087008969 EamA-like transporter family; Region: EamA; pfam00892 159087008970 Hemerythrin-like domain; Region: Hr-like; cd12108 159087008971 Fe binding site [ion binding]; other site 159087008972 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087008973 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087008974 Walker A/P-loop; other site 159087008975 ATP binding site [chemical binding]; other site 159087008976 Q-loop/lid; other site 159087008977 ABC transporter signature motif; other site 159087008978 Walker B; other site 159087008979 D-loop; other site 159087008980 H-loop/switch region; other site 159087008981 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087008982 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087008983 Walker A/P-loop; other site 159087008984 ATP binding site [chemical binding]; other site 159087008985 Q-loop/lid; other site 159087008986 ABC transporter signature motif; other site 159087008987 Walker B; other site 159087008988 D-loop; other site 159087008989 H-loop/switch region; other site 159087008990 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087008991 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087008992 TM-ABC transporter signature motif; other site 159087008993 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 159087008994 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087008995 TM-ABC transporter signature motif; other site 159087008996 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 159087008997 Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; Region: PBP1_alkylbenzenes_like; cd06360 159087008998 putative ligand binding site [chemical binding]; other site 159087008999 4-oxalocrotonate decarboxylase; Region: catechol_dmpH; TIGR03218 159087009000 2-oxopent-4-enoate hydratase; Region: catechol_dmpE; TIGR03220 159087009001 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 159087009002 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 159087009003 NAD binding site [chemical binding]; other site 159087009004 catalytic residues [active] 159087009005 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 159087009006 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 159087009007 tetramer interface [polypeptide binding]; other site 159087009008 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 159087009009 tetramer interface [polypeptide binding]; other site 159087009010 active site 159087009011 Fe binding site [ion binding]; other site 159087009012 2-oxoacid ferredoxin oxidoreductase; Provisional; Region: PRK13030 159087009013 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 159087009014 dimer interface [polypeptide binding]; other site 159087009015 PYR/PP interface [polypeptide binding]; other site 159087009016 TPP binding site [chemical binding]; other site 159087009017 substrate binding site [chemical binding]; other site 159087009018 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 159087009019 TPP-binding site; other site 159087009020 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 159087009021 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 159087009022 Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to...; Region: Rieske_RO_Alpha_HBDO; cd03542 159087009023 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 159087009024 putative alpha subunit interface [polypeptide binding]; other site 159087009025 putative active site [active] 159087009026 putative substrate binding site [chemical binding]; other site 159087009027 Fe binding site [ion binding]; other site 159087009028 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 159087009029 inter-subunit interface; other site 159087009030 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 159087009031 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 159087009032 catalytic loop [active] 159087009033 iron binding site [ion binding]; other site 159087009034 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 159087009035 FAD binding pocket [chemical binding]; other site 159087009036 FAD binding motif [chemical binding]; other site 159087009037 phosphate binding motif [ion binding]; other site 159087009038 beta-alpha-beta structure motif; other site 159087009039 NAD binding pocket [chemical binding]; other site 159087009040 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional; Region: benD; PRK12823 159087009041 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase (DHB DH)-like, classical (c) SDR; Region: DHB_DH-like_SDR_c; cd08937 159087009042 putative NAD(P) binding site [chemical binding]; other site 159087009043 active site 159087009044 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 159087009045 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 159087009046 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 159087009047 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 159087009048 putative PBP binding loops; other site 159087009049 dimer interface [polypeptide binding]; other site 159087009050 ABC-ATPase subunit interface; other site 159087009051 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087009052 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 159087009053 Walker A/P-loop; other site 159087009054 ATP binding site [chemical binding]; other site 159087009055 Q-loop/lid; other site 159087009056 ABC transporter signature motif; other site 159087009057 Walker B; other site 159087009058 D-loop; other site 159087009059 H-loop/switch region; other site 159087009060 TOBE domain; Region: TOBE; cl01440 159087009061 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087009062 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 159087009063 N-terminal plug; other site 159087009064 ligand-binding site [chemical binding]; other site 159087009065 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 159087009066 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 159087009067 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 159087009068 dimerization interface [polypeptide binding]; other site 159087009069 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 159087009070 dimer interface [polypeptide binding]; other site 159087009071 phosphorylation site [posttranslational modification] 159087009072 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 159087009073 ATP binding site [chemical binding]; other site 159087009074 Mg2+ binding site [ion binding]; other site 159087009075 G-X-G motif; other site 159087009076 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009077 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 159087009078 active site 159087009079 phosphorylation site [posttranslational modification] 159087009080 intermolecular recognition site; other site 159087009081 dimerization interface [polypeptide binding]; other site 159087009082 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 159087009083 putative binding surface; other site 159087009084 active site 159087009085 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009086 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 159087009087 active site 159087009088 phosphorylation site [posttranslational modification] 159087009089 intermolecular recognition site; other site 159087009090 dimerization interface [polypeptide binding]; other site 159087009091 PAS domain; Region: PAS_9; pfam13426 159087009092 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 159087009093 putative active site [active] 159087009094 heme pocket [chemical binding]; other site 159087009095 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087009096 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087009097 metal binding site [ion binding]; metal-binding site 159087009098 active site 159087009099 I-site; other site 159087009100 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 159087009101 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 159087009102 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 159087009103 N-terminal plug; other site 159087009104 ligand-binding site [chemical binding]; other site 159087009105 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 159087009106 Predicted membrane protein [Function unknown]; Region: COG2261 159087009107 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087009108 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087009109 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 159087009110 putative effector binding pocket; other site 159087009111 dimerization interface [polypeptide binding]; other site 159087009112 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 159087009113 putative active site [active] 159087009114 metal binding site [ion binding]; metal-binding site 159087009115 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 159087009116 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 159087009117 YceI-like domain; Region: YceI; smart00867 159087009118 YceI-like domain; Region: YceI; smart00867 159087009119 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 159087009120 Predicted flavoprotein [General function prediction only]; Region: COG0431 159087009121 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009122 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 159087009123 active site 159087009124 phosphorylation site [posttranslational modification] 159087009125 intermolecular recognition site; other site 159087009126 dimerization interface [polypeptide binding]; other site 159087009127 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009128 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 159087009129 active site 159087009130 phosphorylation site [posttranslational modification] 159087009131 intermolecular recognition site; other site 159087009132 dimerization interface [polypeptide binding]; other site 159087009133 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087009134 Zn2+ binding site [ion binding]; other site 159087009135 Mg2+ binding site [ion binding]; other site 159087009136 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 159087009137 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 159087009138 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087009139 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 159087009140 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 159087009141 Outer membrane efflux protein; Region: OEP; pfam02321 159087009142 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 159087009143 RES domain; Region: RES; smart00953 159087009144 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 159087009145 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 159087009146 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 159087009147 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 159087009148 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087009149 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 159087009150 dimerization interface [polypeptide binding]; other site 159087009151 substrate binding pocket [chemical binding]; other site 159087009152 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087009153 GAF domain; Region: GAF; pfam01590 159087009154 PAS domain S-box; Region: sensory_box; TIGR00229 159087009155 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 159087009156 putative active site [active] 159087009157 heme pocket [chemical binding]; other site 159087009158 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 159087009159 dimer interface [polypeptide binding]; other site 159087009160 phosphorylation site [posttranslational modification] 159087009161 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 159087009162 ATP binding site [chemical binding]; other site 159087009163 Mg2+ binding site [ion binding]; other site 159087009164 G-X-G motif; other site 159087009165 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009166 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 159087009167 active site 159087009168 phosphorylation site [posttranslational modification] 159087009169 intermolecular recognition site; other site 159087009170 dimerization interface [polypeptide binding]; other site 159087009171 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 159087009172 Dihaem cytochrome c; Region: DHC; pfam09626 159087009173 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 159087009174 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087009175 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 159087009176 active site 159087009177 phosphorylation site [posttranslational modification] 159087009178 intermolecular recognition site; other site 159087009179 dimerization interface [polypeptide binding]; other site 159087009180 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 159087009181 DNA binding site [nucleotide binding] 159087009182 sensor protein QseC; Provisional; Region: PRK10337 159087009183 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 159087009184 dimer interface [polypeptide binding]; other site 159087009185 phosphorylation site [posttranslational modification] 159087009186 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 159087009187 ATP binding site [chemical binding]; other site 159087009188 Mg2+ binding site [ion binding]; other site 159087009189 G-X-G motif; other site 159087009190 H+ Antiporter protein; Region: 2A0121; TIGR00900 159087009191 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 159087009192 putative substrate translocation pore; other site 159087009193 acyl-CoA synthetase; Validated; Region: PRK09088 159087009194 O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE); Region: OSB_CoA_lg; cd05912 159087009195 acyl-activating enzyme (AAE) consensus motif; other site 159087009196 putative AMP binding site [chemical binding]; other site 159087009197 putative active site [active] 159087009198 putative CoA binding site [chemical binding]; other site 159087009199 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 159087009200 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 159087009201 polyphosphate kinase; Provisional; Region: PRK05443 159087009202 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 159087009203 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 159087009204 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 159087009205 putative domain interface [polypeptide binding]; other site 159087009206 putative active site [active] 159087009207 catalytic site [active] 159087009208 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 159087009209 putative domain interface [polypeptide binding]; other site 159087009210 putative active site [active] 159087009211 catalytic site [active] 159087009212 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009213 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 159087009214 active site 159087009215 phosphorylation site [posttranslational modification] 159087009216 intermolecular recognition site; other site 159087009217 dimerization interface [polypeptide binding]; other site 159087009218 PAS domain S-box; Region: sensory_box; TIGR00229 159087009219 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 159087009220 putative active site [active] 159087009221 heme pocket [chemical binding]; other site 159087009222 PAS fold; Region: PAS_4; pfam08448 159087009223 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 159087009224 putative active site [active] 159087009225 heme pocket [chemical binding]; other site 159087009226 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087009227 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087009228 metal binding site [ion binding]; metal-binding site 159087009229 active site 159087009230 I-site; other site 159087009231 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 159087009232 HD domain; Region: HD_4; pfam13328 159087009233 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 159087009234 synthetase active site [active] 159087009235 NTP binding site [chemical binding]; other site 159087009236 metal binding site [ion binding]; metal-binding site 159087009237 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 159087009238 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 159087009239 EamA-like transporter family; Region: EamA; pfam00892 159087009240 EamA-like transporter family; Region: EamA; pfam00892 159087009241 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 159087009242 Alpha/beta hydrolase of unknown function (DUF1057); Region: DUF1057; pfam06342 159087009243 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087009244 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 159087009245 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087009246 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cl00309 159087009247 ComEC family competence protein; Provisional; Region: PRK11539 159087009248 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 159087009249 Competence protein; Region: Competence; pfam03772 159087009250 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 159087009251 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 159087009252 dimerization interface [polypeptide binding]; other site 159087009253 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 159087009254 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087009255 dimer interface [polypeptide binding]; other site 159087009256 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 159087009257 putative CheW interface [polypeptide binding]; other site 159087009258 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 159087009259 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 159087009260 Walker A/P-loop; other site 159087009261 ATP binding site [chemical binding]; other site 159087009262 Q-loop/lid; other site 159087009263 ABC transporter signature motif; other site 159087009264 Walker B; other site 159087009265 D-loop; other site 159087009266 H-loop/switch region; other site 159087009267 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 159087009268 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087009269 FtsX-like permease family; Region: FtsX; pfam02687 159087009270 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 159087009271 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 159087009272 DHH family; Region: DHH; pfam01368 159087009273 DHHA1 domain; Region: DHHA1; pfam02272 159087009274 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK07565 159087009275 Dihydroorotate dehydrogenase (DHOD) like proteins. 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...; Region: DHOD_like; cd04739 159087009276 putative active site [active] 159087009277 putative FMN binding site [chemical binding]; other site 159087009278 putative substrate binding site [chemical binding]; other site 159087009279 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 159087009280 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 159087009281 dimer interface [polypeptide binding]; other site 159087009282 PYR/PP interface [polypeptide binding]; other site 159087009283 TPP binding site [chemical binding]; other site 159087009284 substrate binding site [chemical binding]; other site 159087009285 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 159087009286 Domain of unknown function; Region: EKR; pfam10371 159087009287 4Fe-4S binding domain; Region: Fer4_6; pfam12837 159087009288 4Fe-4S binding domain; Region: Fer4; pfam00037 159087009289 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 159087009290 TPP-binding site [chemical binding]; other site 159087009291 dimer interface [polypeptide binding]; other site 159087009292 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087009293 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 159087009294 putative active site [active] 159087009295 heme pocket [chemical binding]; other site 159087009296 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 159087009297 putative active site [active] 159087009298 heme pocket [chemical binding]; other site 159087009299 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087009300 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087009301 metal binding site [ion binding]; metal-binding site 159087009302 active site 159087009303 I-site; other site 159087009304 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 159087009305 Protein of unknown function (DUF2665); Region: DUF2665; pfam11654 159087009306 Nitrate and nitrite sensing; Region: NIT; pfam08376 159087009307 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087009308 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087009309 dimer interface [polypeptide binding]; other site 159087009310 putative CheW interface [polypeptide binding]; other site 159087009311 peptide chain release factor 2; Provisional; Region: PRK07342 159087009312 This domain is found in peptide chain release factors; Region: PCRF; smart00937 159087009313 RF-1 domain; Region: RF-1; pfam00472 159087009314 Predicted periplasmic lipoprotein (DUF2279); Region: DUF2279; pfam10043 159087009315 Cupin domain; Region: Cupin_2; pfam07883 159087009316 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009317 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 159087009318 active site 159087009319 phosphorylation site [posttranslational modification] 159087009320 intermolecular recognition site; other site 159087009321 dimerization interface [polypeptide binding]; other site 159087009322 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009323 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 159087009324 active site 159087009325 phosphorylation site [posttranslational modification] 159087009326 intermolecular recognition site; other site 159087009327 dimerization interface [polypeptide binding]; other site 159087009328 PAS domain S-box; Region: sensory_box; TIGR00229 159087009329 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 159087009330 dimer interface [polypeptide binding]; other site 159087009331 phosphorylation site [posttranslational modification] 159087009332 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 159087009333 ATP binding site [chemical binding]; other site 159087009334 Mg2+ binding site [ion binding]; other site 159087009335 G-X-G motif; other site 159087009336 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 159087009337 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009338 active site 159087009339 phosphorylation site [posttranslational modification] 159087009340 intermolecular recognition site; other site 159087009341 dimerization interface [polypeptide binding]; other site 159087009342 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 159087009343 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 159087009344 dimer interface [polypeptide binding]; other site 159087009345 putative anticodon binding site; other site 159087009346 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 159087009347 motif 1; other site 159087009348 active site 159087009349 motif 2; other site 159087009350 motif 3; other site 159087009351 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 159087009352 Uncharacterized conserved protein [Function unknown]; Region: COG4121 159087009353 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 159087009354 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 159087009355 homodimer interface [polypeptide binding]; other site 159087009356 substrate-cofactor binding pocket; other site 159087009357 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087009358 catalytic residue [active] 159087009359 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 159087009360 catalytic residue [active] 159087009361 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 159087009362 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087009363 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087009364 Zn2+ binding site [ion binding]; other site 159087009365 Mg2+ binding site [ion binding]; other site 159087009366 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 159087009367 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087009368 Zn2+ binding site [ion binding]; other site 159087009369 Mg2+ binding site [ion binding]; other site 159087009370 Predicted ATPase [General function prediction only]; Region: COG1485 159087009371 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087009372 Walker B; other site 159087009373 D-loop; other site 159087009374 H-loop/switch region; other site 159087009375 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 159087009376 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 159087009377 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 159087009378 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 159087009379 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 159087009380 E3 interaction surface; other site 159087009381 lipoyl attachment site [posttranslational modification]; other site 159087009382 e3 binding domain; Region: E3_binding; pfam02817 159087009383 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 159087009384 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 159087009385 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 159087009386 TPP-binding site [chemical binding]; other site 159087009387 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 159087009388 dimer interface [polypeptide binding]; other site 159087009389 PYR/PP interface [polypeptide binding]; other site 159087009390 TPP binding site [chemical binding]; other site 159087009391 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 159087009392 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 159087009393 dimer interface [polypeptide binding]; other site 159087009394 active site 159087009395 citrylCoA binding site [chemical binding]; other site 159087009396 NADH binding [chemical binding]; other site 159087009397 cationic pore residues; other site 159087009398 oxalacetate/citrate binding site [chemical binding]; other site 159087009399 coenzyme A binding site [chemical binding]; other site 159087009400 catalytic triad [active] 159087009401 Flavinator of succinate dehydrogenase; Region: Sdh5; pfam03937 159087009402 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 159087009403 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 159087009404 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 159087009405 L-aspartate oxidase; Provisional; Region: PRK06175 159087009406 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 159087009407 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 159087009408 SdhC subunit interface [polypeptide binding]; other site 159087009409 proximal heme binding site [chemical binding]; other site 159087009410 cardiolipin binding site; other site 159087009411 Iron-sulfur protein interface; other site 159087009412 proximal quinone binding site [chemical binding]; other site 159087009413 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 159087009414 Iron-sulfur protein interface; other site 159087009415 proximal quinone binding site [chemical binding]; other site 159087009416 SdhD (CybS) interface [polypeptide binding]; other site 159087009417 proximal heme binding site [chemical binding]; other site 159087009418 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 159087009419 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087009420 DNA-binding site [nucleotide binding]; DNA binding site 159087009421 UTRA domain; Region: UTRA; pfam07702 159087009422 malate dehydrogenase; Provisional; Region: PRK05442 159087009423 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 159087009424 NAD(P) binding site [chemical binding]; other site 159087009425 dimer interface [polypeptide binding]; other site 159087009426 malate binding site [chemical binding]; other site 159087009427 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 159087009428 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 159087009429 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 159087009430 probable active site [active] 159087009431 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 159087009432 FOG: CBS domain [General function prediction only]; Region: COG0517 159087009433 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 159087009434 FMN binding site [chemical binding]; other site 159087009435 substrate binding site [chemical binding]; other site 159087009436 putative catalytic residue [active] 159087009437 NnrS protein; Region: NnrS; pfam05940 159087009438 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 159087009439 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 159087009440 S-adenosylmethionine binding site [chemical binding]; other site 159087009441 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 159087009442 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 159087009443 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087009444 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 159087009445 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 159087009446 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087009447 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087009448 metal binding site [ion binding]; metal-binding site 159087009449 active site 159087009450 I-site; other site 159087009451 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_13; cd06324 159087009452 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 159087009453 putative ligand binding site [chemical binding]; other site 159087009454 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 159087009455 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 159087009456 substrate binding site [chemical binding]; other site 159087009457 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 159087009458 substrate binding site [chemical binding]; other site 159087009459 ligand binding site [chemical binding]; other site 159087009460 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 159087009461 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087009462 dimer interface [polypeptide binding]; other site 159087009463 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 159087009464 putative CheW interface [polypeptide binding]; other site 159087009465 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 159087009466 Putative methyltransferase; Region: Methyltransf_4; cl17290 159087009467 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 159087009468 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 159087009469 FMN binding site [chemical binding]; other site 159087009470 active site 159087009471 catalytic residues [active] 159087009472 substrate binding site [chemical binding]; other site 159087009473 PIN domain; Region: PIN_3; pfam13470 159087009474 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 159087009475 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 159087009476 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 159087009477 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 159087009478 Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing...; Region: H2MP; cd00518 159087009479 nickel binding site [ion binding]; other site 159087009480 PAS domain; Region: PAS_9; pfam13426 159087009481 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 159087009482 dimer interface [polypeptide binding]; other site 159087009483 phosphorylation site [posttranslational modification] 159087009484 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 159087009485 ATP binding site [chemical binding]; other site 159087009486 Mg2+ binding site [ion binding]; other site 159087009487 G-X-G motif; other site 159087009488 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009489 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 159087009490 active site 159087009491 phosphorylation site [posttranslational modification] 159087009492 intermolecular recognition site; other site 159087009493 dimerization interface [polypeptide binding]; other site 159087009494 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009495 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 159087009496 active site 159087009497 phosphorylation site [posttranslational modification] 159087009498 intermolecular recognition site; other site 159087009499 dimerization interface [polypeptide binding]; other site 159087009500 Cache domain; Region: Cache_1; pfam02743 159087009501 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087009502 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 159087009503 dimer interface [polypeptide binding]; other site 159087009504 phosphorylation site [posttranslational modification] 159087009505 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 159087009506 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 159087009507 ATP binding site [chemical binding]; other site 159087009508 Mg2+ binding site [ion binding]; other site 159087009509 G-X-G motif; other site 159087009510 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087009511 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 159087009512 active site 159087009513 phosphorylation site [posttranslational modification] 159087009514 intermolecular recognition site; other site 159087009515 dimerization interface [polypeptide binding]; other site 159087009516 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009517 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 159087009518 active site 159087009519 phosphorylation site [posttranslational modification] 159087009520 intermolecular recognition site; other site 159087009521 dimerization interface [polypeptide binding]; other site 159087009522 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 159087009523 active site residue [active] 159087009524 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 159087009525 active site residue [active] 159087009526 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 159087009527 active site residue [active] 159087009528 hypothetical protein; Validated; Region: PRK02101 159087009529 Protein of unknown function (DUF2863); Region: DUF2863; pfam11062 159087009530 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 159087009531 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 159087009532 inhibitor-cofactor binding pocket; inhibition site 159087009533 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087009534 catalytic residue [active] 159087009535 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 159087009536 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 159087009537 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 159087009538 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 159087009539 substrate-cofactor binding pocket; other site 159087009540 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087009541 catalytic residue [active] 159087009542 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 159087009543 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 159087009544 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 159087009545 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 159087009546 S-adenosylmethionine binding site [chemical binding]; other site 159087009547 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 159087009548 AAA domain; Region: AAA_26; pfam13500 159087009549 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 159087009550 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 159087009551 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087009552 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 159087009553 active site 159087009554 phosphorylation site [posttranslational modification] 159087009555 intermolecular recognition site; other site 159087009556 dimerization interface [polypeptide binding]; other site 159087009557 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087009558 Zn2+ binding site [ion binding]; other site 159087009559 Mg2+ binding site [ion binding]; other site 159087009560 intracellular septation protein A; Reviewed; Region: PRK00259 159087009561 YciI-like protein; Reviewed; Region: PRK11370 159087009562 BolA-like protein; Region: BolA; pfam01722 159087009563 SurA N-terminal domain; Region: SurA_N_3; cl07813 159087009564 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 159087009565 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 159087009566 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 159087009567 HDOD domain; Region: HDOD; pfam08668 159087009568 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 159087009569 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12683 159087009570 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087009571 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 159087009572 substrate binding site [chemical binding]; other site 159087009573 dimerization interface [polypeptide binding]; other site 159087009574 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087009575 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 159087009576 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 159087009577 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 159087009578 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 159087009579 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 159087009580 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 159087009581 Active Sites [active] 159087009582 Haemolytic domain; Region: Haemolytic; cl00506 159087009583 Predicted transcriptional regulator [Transcription]; Region: COG1959 159087009584 Transcriptional regulator; Region: Rrf2; cl17282 159087009585 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 159087009586 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087009587 4Fe-4S binding domain; Region: Fer4; pfam00037 159087009588 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 159087009589 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 159087009590 Transglycosylase; Region: Transgly; cl17702 159087009591 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 159087009592 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087009593 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 159087009594 ligand binding site [chemical binding]; other site 159087009595 flexible hinge region; other site 159087009596 Acetokinase family; Region: Acetate_kinase; cl17229 159087009597 propionate/acetate kinase; Provisional; Region: PRK12379 159087009598 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 159087009599 Propanediol utilisation protein PduL; Region: PduL; pfam06130 159087009600 Propanediol utilisation protein PduL; Region: PduL; pfam06130 159087009601 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087009602 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087009603 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 159087009604 active site 159087009605 phosphorylation site [posttranslational modification] 159087009606 intermolecular recognition site; other site 159087009607 dimerization interface [polypeptide binding]; other site 159087009608 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 159087009609 Walker A motif; other site 159087009610 ATP binding site [chemical binding]; other site 159087009611 Walker B motif; other site 159087009612 arginine finger; other site 159087009613 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087009614 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087009615 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 159087009616 dimerization interface [polypeptide binding]; other site 159087009617 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 159087009618 dimer interface [polypeptide binding]; other site 159087009619 phosphorylation site [posttranslational modification] 159087009620 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 159087009621 ATP binding site [chemical binding]; other site 159087009622 Mg2+ binding site [ion binding]; other site 159087009623 G-X-G motif; other site 159087009624 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087009625 ligand binding site [chemical binding]; other site 159087009626 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087009627 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 159087009628 ligand binding site [chemical binding]; other site 159087009629 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 159087009630 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 159087009631 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 159087009632 uncharacterized domain; Region: TIGR00702 159087009633 YcaO-like family; Region: YcaO; pfam02624 159087009634 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 159087009635 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087009636 HAMP domain; Region: HAMP; pfam00672 159087009637 dimerization interface [polypeptide binding]; other site 159087009638 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087009639 dimer interface [polypeptide binding]; other site 159087009640 putative CheW interface [polypeptide binding]; other site 159087009641 CHASE domain; Region: CHASE; cl01369 159087009642 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087009643 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 159087009644 putative active site [active] 159087009645 heme pocket [chemical binding]; other site 159087009646 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 159087009647 putative active site [active] 159087009648 heme pocket [chemical binding]; other site 159087009649 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 159087009650 dimer interface [polypeptide binding]; other site 159087009651 phosphorylation site [posttranslational modification] 159087009652 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 159087009653 ATP binding site [chemical binding]; other site 159087009654 Mg2+ binding site [ion binding]; other site 159087009655 G-X-G motif; other site 159087009656 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009657 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 159087009658 active site 159087009659 phosphorylation site [posttranslational modification] 159087009660 intermolecular recognition site; other site 159087009661 dimerization interface [polypeptide binding]; other site 159087009662 fumarate hydratase; Reviewed; Region: fumC; PRK00485 159087009663 Class II fumarases; Region: Fumarase_classII; cd01362 159087009664 active site 159087009665 tetramer interface [polypeptide binding]; other site 159087009666 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 159087009667 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 159087009668 Cytochrome c; Region: Cytochrom_C; cl11414 159087009669 TIR domain; Region: TIR_2; pfam13676 159087009670 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087009671 ligand binding site [chemical binding]; other site 159087009672 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 159087009673 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 159087009674 E-class dimer interface [polypeptide binding]; other site 159087009675 P-class dimer interface [polypeptide binding]; other site 159087009676 active site 159087009677 Cu2+ binding site [ion binding]; other site 159087009678 Zn2+ binding site [ion binding]; other site 159087009679 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 159087009680 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 159087009681 Active Sites [active] 159087009682 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 159087009683 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 159087009684 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 159087009685 CysD dimerization site [polypeptide binding]; other site 159087009686 G1 box; other site 159087009687 putative GEF interaction site [polypeptide binding]; other site 159087009688 GTP/Mg2+ binding site [chemical binding]; other site 159087009689 Switch I region; other site 159087009690 G2 box; other site 159087009691 G3 box; other site 159087009692 Switch II region; other site 159087009693 G4 box; other site 159087009694 G5 box; other site 159087009695 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 159087009696 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 159087009697 HAMP domain; Region: HAMP; pfam00672 159087009698 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 159087009699 dimer interface [polypeptide binding]; other site 159087009700 phosphorylation site [posttranslational modification] 159087009701 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 159087009702 ATP binding site [chemical binding]; other site 159087009703 Mg2+ binding site [ion binding]; other site 159087009704 G-X-G motif; other site 159087009705 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009706 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 159087009707 active site 159087009708 phosphorylation site [posttranslational modification] 159087009709 intermolecular recognition site; other site 159087009710 dimerization interface [polypeptide binding]; other site 159087009711 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087009712 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 159087009713 ligand binding site [chemical binding]; other site 159087009714 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 159087009715 catalytic residues [active] 159087009716 Predicted permeases [General function prediction only]; Region: COG0701 159087009717 RNA polymerase sigma factor, SigZ family; Region: SigZ; TIGR02959 159087009718 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087009719 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 159087009720 DNA binding residues [nucleotide binding] 159087009721 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 159087009722 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087009723 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 159087009724 N-terminal plug; other site 159087009725 ligand-binding site [chemical binding]; other site 159087009726 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 159087009727 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 159087009728 N-terminal plug; other site 159087009729 ligand-binding site [chemical binding]; other site 159087009730 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 159087009731 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 159087009732 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087009733 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087009734 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087009735 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087009736 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 159087009737 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087009738 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009739 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 159087009740 active site 159087009741 phosphorylation site [posttranslational modification] 159087009742 intermolecular recognition site; other site 159087009743 dimerization interface [polypeptide binding]; other site 159087009744 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 159087009745 interface (dimer of trimers) [polypeptide binding]; other site 159087009746 Substrate-binding/catalytic site; other site 159087009747 Zn-binding sites [ion binding]; other site 159087009748 Isochorismatase family; Region: Isochorismatase; pfam00857 159087009749 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 159087009750 catalytic triad [active] 159087009751 conserved cis-peptide bond; other site 159087009752 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 159087009753 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087009754 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087009755 metal binding site [ion binding]; metal-binding site 159087009756 active site 159087009757 I-site; other site 159087009758 Protein of unknown function, DUF599; Region: DUF599; pfam04654 159087009759 Predicted permeases [General function prediction only]; Region: RarD; COG2962 159087009760 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 159087009761 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 159087009762 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 159087009763 Hemerythrin; Region: Hemerythrin; cd12107 159087009764 Fe binding site [ion binding]; other site 159087009765 ribonuclease R; Region: RNase_R; TIGR02063 159087009766 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 159087009767 RNB domain; Region: RNB; pfam00773 159087009768 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 159087009769 RNA binding site [nucleotide binding]; other site 159087009770 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 159087009771 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 159087009772 GDP-binding site [chemical binding]; other site 159087009773 ACT binding site; other site 159087009774 IMP binding site; other site 159087009775 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 159087009776 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 159087009777 dimer interface [polypeptide binding]; other site 159087009778 motif 1; other site 159087009779 active site 159087009780 motif 2; other site 159087009781 motif 3; other site 159087009782 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 159087009783 FtsH protease regulator HflC; Provisional; Region: PRK11029 159087009784 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 159087009785 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 159087009786 HflK protein; Region: hflK; TIGR01933 159087009787 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 159087009788 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 159087009789 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 159087009790 HflX GTPase family; Region: HflX; cd01878 159087009791 G1 box; other site 159087009792 GTP/Mg2+ binding site [chemical binding]; other site 159087009793 Switch I region; other site 159087009794 G2 box; other site 159087009795 G3 box; other site 159087009796 Switch II region; other site 159087009797 G4 box; other site 159087009798 G5 box; other site 159087009799 bacterial Hfq-like; Region: Hfq; cd01716 159087009800 hexamer interface [polypeptide binding]; other site 159087009801 Sm1 motif; other site 159087009802 RNA binding site [nucleotide binding]; other site 159087009803 Sm2 motif; other site 159087009804 GTP-binding protein Der; Reviewed; Region: PRK00093 159087009805 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 159087009806 G1 box; other site 159087009807 GTP/Mg2+ binding site [chemical binding]; other site 159087009808 Switch I region; other site 159087009809 G2 box; other site 159087009810 Switch II region; other site 159087009811 G3 box; other site 159087009812 G4 box; other site 159087009813 G5 box; other site 159087009814 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 159087009815 G1 box; other site 159087009816 GTP/Mg2+ binding site [chemical binding]; other site 159087009817 Switch I region; other site 159087009818 G2 box; other site 159087009819 G3 box; other site 159087009820 Switch II region; other site 159087009821 G4 box; other site 159087009822 G5 box; other site 159087009823 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 159087009824 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 159087009825 Trp docking motif [polypeptide binding]; other site 159087009826 active site 159087009827 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 159087009828 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 159087009829 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 159087009830 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 159087009831 dimer interface [polypeptide binding]; other site 159087009832 motif 1; other site 159087009833 active site 159087009834 motif 2; other site 159087009835 motif 3; other site 159087009836 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 159087009837 anticodon binding site; other site 159087009838 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 159087009839 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 159087009840 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 159087009841 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 159087009842 Helix-turn-helix domain; Region: HTH_25; pfam13413 159087009843 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 159087009844 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 159087009845 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 159087009846 binding surface 159087009847 TPR motif; other site 159087009848 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 159087009849 binding surface 159087009850 TPR motif; other site 159087009851 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 159087009852 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 159087009853 FeS/SAM binding site; other site 159087009854 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 159087009855 active site 159087009856 multimer interface [polypeptide binding]; other site 159087009857 DctM-like transporters; Region: DctM; pfam06808 159087009858 TRAP transporter, DctM subunit; Region: dctM; TIGR00786 159087009859 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 159087009860 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 159087009861 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 159087009862 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 159087009863 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 159087009864 PAS domain S-box; Region: sensory_box; TIGR00229 159087009865 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 159087009866 putative active site [active] 159087009867 heme pocket [chemical binding]; other site 159087009868 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 159087009869 dimer interface [polypeptide binding]; other site 159087009870 phosphorylation site [posttranslational modification] 159087009871 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 159087009872 ATP binding site [chemical binding]; other site 159087009873 Mg2+ binding site [ion binding]; other site 159087009874 G-X-G motif; other site 159087009875 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087009876 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 159087009877 active site 159087009878 phosphorylation site [posttranslational modification] 159087009879 intermolecular recognition site; other site 159087009880 dimerization interface [polypeptide binding]; other site 159087009881 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 159087009882 DNA binding residues [nucleotide binding] 159087009883 dimerization interface [polypeptide binding]; other site 159087009884 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 159087009885 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 159087009886 catalytic residues [active] 159087009887 transcription termination factor Rho; Provisional; Region: rho; PRK09376 159087009888 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 159087009889 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 159087009890 RNA binding site [nucleotide binding]; other site 159087009891 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 159087009892 multimer interface [polypeptide binding]; other site 159087009893 Walker A motif; other site 159087009894 ATP binding site [chemical binding]; other site 159087009895 Walker B motif; other site 159087009896 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 159087009897 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 159087009898 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 159087009899 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 159087009900 catalytic site [active] 159087009901 putative active site [active] 159087009902 putative substrate binding site [chemical binding]; other site 159087009903 dimer interface [polypeptide binding]; other site 159087009904 Peptidase family M48; Region: Peptidase_M48; pfam01435 159087009905 GTPase RsgA; Reviewed; Region: PRK00098 159087009906 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 159087009907 RNA binding site [nucleotide binding]; other site 159087009908 homodimer interface [polypeptide binding]; other site 159087009909 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 159087009910 GTPase/Zn-binding domain interface [polypeptide binding]; other site 159087009911 GTP/Mg2+ binding site [chemical binding]; other site 159087009912 G4 box; other site 159087009913 G5 box; other site 159087009914 G1 box; other site 159087009915 Switch I region; other site 159087009916 G2 box; other site 159087009917 G3 box; other site 159087009918 Switch II region; other site 159087009919 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087009920 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 159087009921 active site 159087009922 phosphorylation site [posttranslational modification] 159087009923 intermolecular recognition site; other site 159087009924 dimerization interface [polypeptide binding]; other site 159087009925 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087009926 Zn2+ binding site [ion binding]; other site 159087009927 Mg2+ binding site [ion binding]; other site 159087009928 FOG: CBS domain [General function prediction only]; Region: COG0517 159087009929 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 159087009930 FOG: CBS domain [General function prediction only]; Region: COG0517 159087009931 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 159087009932 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 159087009933 PAS fold; Region: PAS_3; pfam08447 159087009934 putative active site [active] 159087009935 heme pocket [chemical binding]; other site 159087009936 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087009937 GAF domain; Region: GAF; pfam01590 159087009938 PAS fold; Region: PAS_3; pfam08447 159087009939 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 159087009940 putative active site [active] 159087009941 heme pocket [chemical binding]; other site 159087009942 PAS fold; Region: PAS_3; pfam08447 159087009943 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 159087009944 putative active site [active] 159087009945 heme pocket [chemical binding]; other site 159087009946 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087009947 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 159087009948 putative active site [active] 159087009949 heme pocket [chemical binding]; other site 159087009950 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 159087009951 dimer interface [polypeptide binding]; other site 159087009952 phosphorylation site [posttranslational modification] 159087009953 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 159087009954 ATP binding site [chemical binding]; other site 159087009955 Mg2+ binding site [ion binding]; other site 159087009956 G-X-G motif; other site 159087009957 Response regulator receiver domain; Region: Response_reg; pfam00072 159087009958 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 159087009959 active site 159087009960 phosphorylation site [posttranslational modification] 159087009961 intermolecular recognition site; other site 159087009962 dimerization interface [polypeptide binding]; other site 159087009963 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 159087009964 putative binding surface; other site 159087009965 active site 159087009966 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 159087009967 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 159087009968 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 159087009969 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 159087009970 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 159087009971 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 159087009972 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 159087009973 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 159087009974 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 159087009975 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 159087009976 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 159087009977 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 159087009978 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 159087009979 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_10; cd07251 159087009980 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 159087009981 Flagellin N-methylase; Region: FliB; cl00497 159087009982 ParB-like nuclease domain; Region: ParB; smart00470 159087009983 Cytochrome C' Region: Cytochrom_C_2; pfam01322 159087009984 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 159087009985 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087009986 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 159087009987 dimer interface [polypeptide binding]; other site 159087009988 phosphorylation site [posttranslational modification] 159087009989 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 159087009990 ATP binding site [chemical binding]; other site 159087009991 Mg2+ binding site [ion binding]; other site 159087009992 G-X-G motif; other site 159087009993 HI0933-like protein; Region: HI0933_like; pfam03486 159087009994 Phasin protein; Region: Phasin_2; pfam09361 159087009995 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 159087009996 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 159087009997 Uncharacterized conserved protein [Function unknown]; Region: COG2308 159087009998 beta-ketothiolase; Provisional; Region: PRK09051 159087009999 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 159087010000 dimer interface [polypeptide binding]; other site 159087010001 active site 159087010002 CobD/CbiB family protein; Provisional; Region: PRK07630 159087010003 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 159087010004 putative active site [active] 159087010005 putative CoA binding site [chemical binding]; other site 159087010006 nudix motif; other site 159087010007 metal binding site [ion binding]; metal-binding site 159087010008 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 159087010009 catalytic motif [active] 159087010010 Catalytic residue [active] 159087010011 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 159087010012 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 159087010013 catalytic triad [active] 159087010014 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 159087010015 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 159087010016 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 159087010017 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 159087010018 argininosuccinate synthase; Provisional; Region: PRK13820 159087010019 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 159087010020 ANP binding site [chemical binding]; other site 159087010021 Substrate Binding Site II [chemical binding]; other site 159087010022 Substrate Binding Site I [chemical binding]; other site 159087010023 ornithine carbamoyltransferase; Provisional; Region: PRK00779 159087010024 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 159087010025 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 159087010026 acetylornithine aminotransferase; Provisional; Region: PRK02627 159087010027 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 159087010028 inhibitor-cofactor binding pocket; inhibition site 159087010029 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087010030 catalytic residue [active] 159087010031 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 159087010032 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 159087010033 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 159087010034 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 159087010035 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 159087010036 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 159087010037 Type II transport protein GspH; Region: GspH; pfam12019 159087010038 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 159087010039 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 159087010040 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 159087010041 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 159087010042 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 159087010043 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 159087010044 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 159087010045 lipoprotein signal peptidase; Provisional; Region: PRK14787 159087010046 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 159087010047 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087010048 active site 159087010049 HIGH motif; other site 159087010050 nucleotide binding site [chemical binding]; other site 159087010051 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 159087010052 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 159087010053 active site 159087010054 KMSKS motif; other site 159087010055 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 159087010056 tRNA binding surface [nucleotide binding]; other site 159087010057 anticodon binding site; other site 159087010058 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 159087010059 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 159087010060 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 159087010061 active site 159087010062 Riboflavin kinase; Region: Flavokinase; pfam01687 159087010063 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087010064 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010065 metal binding site [ion binding]; metal-binding site 159087010066 active site 159087010067 I-site; other site 159087010068 AMIN domain; Region: AMIN; pfam11741 159087010069 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 159087010070 active site 159087010071 metal binding site [ion binding]; metal-binding site 159087010072 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 159087010073 epoxyqueuosine reductase; Region: TIGR00276 159087010074 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 159087010075 This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases; Region: CHASE; smart01079 159087010076 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087010077 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010078 metal binding site [ion binding]; metal-binding site 159087010079 active site 159087010080 I-site; other site 159087010081 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 159087010082 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 159087010083 active site residue [active] 159087010084 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 159087010085 active site residue [active] 159087010086 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 159087010087 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 159087010088 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 159087010089 [2Fe-2S] cluster binding site [ion binding]; other site 159087010090 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 159087010091 alpha subunit interface [polypeptide binding]; other site 159087010092 active site 159087010093 substrate binding site [chemical binding]; other site 159087010094 Fe binding site [ion binding]; other site 159087010095 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 159087010096 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 159087010097 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 159087010098 substrate binding pocket [chemical binding]; other site 159087010099 chain length determination region; other site 159087010100 substrate-Mg2+ binding site; other site 159087010101 catalytic residues [active] 159087010102 aspartate-rich region 1; other site 159087010103 active site lid residues [active] 159087010104 aspartate-rich region 2; other site 159087010105 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 159087010106 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 159087010107 TPP-binding site; other site 159087010108 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 159087010109 PYR/PP interface [polypeptide binding]; other site 159087010110 dimer interface [polypeptide binding]; other site 159087010111 TPP binding site [chemical binding]; other site 159087010112 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 159087010113 putative GTP cyclohydrolase; Provisional; Region: PRK13674 159087010114 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 159087010115 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 159087010116 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 159087010117 RimM N-terminal domain; Region: RimM; pfam01782 159087010118 PRC-barrel domain; Region: PRC; pfam05239 159087010119 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 159087010120 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 159087010121 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 159087010122 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 159087010123 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 159087010124 2-isopropylmalate synthase; Validated; Region: PRK00915 159087010125 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 159087010126 active site 159087010127 catalytic residues [active] 159087010128 metal binding site [ion binding]; metal-binding site 159087010129 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 159087010130 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 159087010131 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 159087010132 ketol-acid reductoisomerase; Provisional; Region: PRK05479 159087010133 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 159087010134 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 159087010135 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 159087010136 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 159087010137 putative valine binding site [chemical binding]; other site 159087010138 dimer interface [polypeptide binding]; other site 159087010139 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 159087010140 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 159087010141 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 159087010142 PYR/PP interface [polypeptide binding]; other site 159087010143 dimer interface [polypeptide binding]; other site 159087010144 TPP binding site [chemical binding]; other site 159087010145 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 159087010146 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 159087010147 TPP-binding site [chemical binding]; other site 159087010148 dimer interface [polypeptide binding]; other site 159087010149 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087010150 RNA polymerase factor sigma-70; Validated; Region: PRK09047 159087010151 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 159087010152 DNA binding residues [nucleotide binding] 159087010153 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 159087010154 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 159087010155 RDD family; Region: RDD; pfam06271 159087010156 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 159087010157 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 159087010158 Predicted permeases [General function prediction only]; Region: COG0795 159087010159 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 159087010160 multifunctional aminopeptidase A; Provisional; Region: PRK00913 159087010161 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 159087010162 interface (dimer of trimers) [polypeptide binding]; other site 159087010163 Substrate-binding/catalytic site; other site 159087010164 Zn-binding sites [ion binding]; other site 159087010165 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 159087010166 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 159087010167 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 159087010168 HIGH motif; other site 159087010169 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 159087010170 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 159087010171 active site 159087010172 KMSKS motif; other site 159087010173 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 159087010174 tRNA binding surface [nucleotide binding]; other site 159087010175 anticodon binding site; other site 159087010176 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 159087010177 aminodeoxychorismate synthase; Provisional; Region: PRK07508 159087010178 chorismate binding enzyme; Region: Chorismate_bind; cl10555 159087010179 hypothetical protein; Provisional; Region: PRK07546 159087010180 substrate-cofactor binding pocket; other site 159087010181 homodimer interface [polypeptide binding]; other site 159087010182 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 159087010183 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087010184 catalytic residue [active] 159087010185 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 159087010186 CPxP motif; other site 159087010187 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 159087010188 Peptidase family M48; Region: Peptidase_M48; cl12018 159087010189 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 159087010190 trimer interface [polypeptide binding]; other site 159087010191 dimer interface [polypeptide binding]; other site 159087010192 putative active site [active] 159087010193 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 159087010194 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 159087010195 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 159087010196 DNA-binding site [nucleotide binding]; DNA binding site 159087010197 RNA-binding motif; other site 159087010198 Uncharacterized conserved protein [Function unknown]; Region: COG2127 159087010199 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 159087010200 Clp amino terminal domain; Region: Clp_N; pfam02861 159087010201 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 159087010202 Walker A motif; other site 159087010203 ATP binding site [chemical binding]; other site 159087010204 Walker B motif; other site 159087010205 arginine finger; other site 159087010206 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 159087010207 Walker A motif; other site 159087010208 ATP binding site [chemical binding]; other site 159087010209 Walker B motif; other site 159087010210 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 159087010211 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 159087010212 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087010213 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 159087010214 dimerization interface [polypeptide binding]; other site 159087010215 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087010216 dimer interface [polypeptide binding]; other site 159087010217 putative CheW interface [polypeptide binding]; other site 159087010218 isocitrate lyase; Provisional; Region: PRK15063 159087010219 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 159087010220 tetramer interface [polypeptide binding]; other site 159087010221 active site 159087010222 Mg2+/Mn2+ binding site [ion binding]; other site 159087010223 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087010224 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 159087010225 PAS domain S-box; Region: sensory_box; TIGR00229 159087010226 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 159087010227 putative active site [active] 159087010228 heme pocket [chemical binding]; other site 159087010229 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 159087010230 PAS domain; Region: PAS_9; pfam13426 159087010231 putative active site [active] 159087010232 heme pocket [chemical binding]; other site 159087010233 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087010234 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010235 metal binding site [ion binding]; metal-binding site 159087010236 active site 159087010237 I-site; other site 159087010238 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 159087010239 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087010240 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087010241 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 159087010242 putative effector binding pocket; other site 159087010243 dimerization interface [polypeptide binding]; other site 159087010244 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 159087010245 malate synthase A; Region: malate_syn_A; TIGR01344 159087010246 active site 159087010247 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 159087010248 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 159087010249 Uncharacterized membrane protein [Function unknown]; Region: SpmB; cl17667 159087010250 LrgA family; Region: LrgA; pfam03788 159087010251 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 159087010252 PAS domain S-box; Region: sensory_box; TIGR00229 159087010253 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 159087010254 putative active site [active] 159087010255 heme pocket [chemical binding]; other site 159087010256 PAS domain; Region: PAS_8; pfam13188 159087010257 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087010258 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 159087010259 dimer interface [polypeptide binding]; other site 159087010260 phosphorylation site [posttranslational modification] 159087010261 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 159087010262 ATP binding site [chemical binding]; other site 159087010263 Mg2+ binding site [ion binding]; other site 159087010264 G-X-G motif; other site 159087010265 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087010266 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 159087010267 active site 159087010268 phosphorylation site [posttranslational modification] 159087010269 intermolecular recognition site; other site 159087010270 dimerization interface [polypeptide binding]; other site 159087010271 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 159087010272 DNA binding residues [nucleotide binding] 159087010273 dimerization interface [polypeptide binding]; other site 159087010274 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087010275 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 159087010276 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087010277 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 159087010278 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 159087010279 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 159087010280 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087010281 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087010282 dimer interface [polypeptide binding]; other site 159087010283 putative CheW interface [polypeptide binding]; other site 159087010284 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 159087010285 CoA-transferase family III; Region: CoA_transf_3; pfam02515 159087010286 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 159087010287 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 159087010288 isocitrate dehydrogenase; Validated; Region: PRK07362 159087010289 isocitrate dehydrogenase; Reviewed; Region: PRK07006 159087010290 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 159087010291 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 159087010292 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 159087010293 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 159087010294 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 159087010295 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 159087010296 ligand binding site [chemical binding]; other site 159087010297 homodimer interface [polypeptide binding]; other site 159087010298 NAD(P) binding site [chemical binding]; other site 159087010299 trimer interface B [polypeptide binding]; other site 159087010300 trimer interface A [polypeptide binding]; other site 159087010301 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 159087010302 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 159087010303 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 159087010304 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 159087010305 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087010306 dimer interface [polypeptide binding]; other site 159087010307 putative CheW interface [polypeptide binding]; other site 159087010308 Predicted transporter component [General function prediction only]; Region: COG2391 159087010309 Sulphur transport; Region: Sulf_transp; pfam04143 159087010310 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 159087010311 active site residue [active] 159087010312 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 159087010313 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 159087010314 active site 159087010315 metal binding site [ion binding]; metal-binding site 159087010316 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 159087010317 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 159087010318 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 159087010319 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 159087010320 Cytochrome c; Region: Cytochrom_C; pfam00034 159087010321 Cytochrome c; Region: Cytochrom_C; cl11414 159087010322 bacterial SoxC is a member of the sulfite oxidase (SO) family of molybdopterin binding domains. SoxC is involved in oxidation of sulfur compounds during chemolithothrophic growth. Together with SoxD, a small c-type heme containing subunit, it forms a...; Region: bact_SoxC_Moco; cd02113 159087010323 Moco binding site; other site 159087010324 metal coordination site [ion binding]; other site 159087010325 dimerization interface [polypeptide binding]; other site 159087010326 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 159087010327 putative DNA binding site [nucleotide binding]; other site 159087010328 dimerization interface [polypeptide binding]; other site 159087010329 putative Zn2+ binding site [ion binding]; other site 159087010330 Cytochrome c; Region: Cytochrom_C; cl11414 159087010331 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 159087010332 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 159087010333 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 159087010334 Cytochrome c; Region: Cytochrom_C; cl11414 159087010335 Cytochrome c; Region: Cytochrom_C; cl11414 159087010336 Cytochrome c553 [Energy production and conversion]; Region: COG2863 159087010337 Cytochrome c; Region: Cytochrom_C; cl11414 159087010338 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 159087010339 trimer interface [polypeptide binding]; other site 159087010340 active site 159087010341 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 159087010342 Flavoprotein; Region: Flavoprotein; pfam02441 159087010343 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 159087010344 hypothetical protein; Reviewed; Region: PRK00024 159087010345 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 159087010346 MPN+ (JAMM) motif; other site 159087010347 Zinc-binding site [ion binding]; other site 159087010348 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 159087010349 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 159087010350 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 159087010351 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 159087010352 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 159087010353 active site 159087010354 phosphorylation site [posttranslational modification] 159087010355 intermolecular recognition site; other site 159087010356 dimerization interface [polypeptide binding]; other site 159087010357 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 159087010358 DNA binding site [nucleotide binding] 159087010359 sensor protein RstB; Provisional; Region: PRK10604 159087010360 HAMP domain; Region: HAMP; pfam00672 159087010361 dimerization interface [polypeptide binding]; other site 159087010362 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 159087010363 dimer interface [polypeptide binding]; other site 159087010364 phosphorylation site [posttranslational modification] 159087010365 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 159087010366 ATP binding site [chemical binding]; other site 159087010367 Mg2+ binding site [ion binding]; other site 159087010368 G-X-G motif; other site 159087010369 RNA polymerase sigma-70 factor, TIGR02943 family; Region: Sig70_famx1 159087010370 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087010371 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 159087010372 Putative zinc-finger; Region: zf-HC2; pfam13490 159087010373 hypothetical protein; Provisional; Region: PRK05409 159087010374 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 159087010375 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 159087010376 catalytic residues [active] 159087010377 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 159087010378 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 159087010379 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 159087010380 Mechanosensitive ion channel; Region: MS_channel; pfam00924 159087010381 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 159087010382 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 159087010383 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 159087010384 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 159087010385 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 159087010386 active site 159087010387 substrate binding site [chemical binding]; other site 159087010388 cosubstrate binding site; other site 159087010389 catalytic site [active] 159087010390 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 159087010391 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 159087010392 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 159087010393 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 159087010394 ATP binding site [chemical binding]; other site 159087010395 Mg2+ binding site [ion binding]; other site 159087010396 G-X-G motif; other site 159087010397 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 159087010398 ATP binding site [chemical binding]; other site 159087010399 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 159087010400 DinB superfamily; Region: DinB_2; pfam12867 159087010401 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 159087010402 putative cation:proton antiport protein; Provisional; Region: PRK10669 159087010403 TrkA-N domain; Region: TrkA_N; pfam02254 159087010404 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 159087010405 Ligand Binding Site [chemical binding]; other site 159087010406 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 159087010407 Ligand Binding Site [chemical binding]; other site 159087010408 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 159087010409 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 159087010410 Response regulator receiver domain; Region: Response_reg; pfam00072 159087010411 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 159087010412 active site 159087010413 phosphorylation site [posttranslational modification] 159087010414 intermolecular recognition site; other site 159087010415 dimerization interface [polypeptide binding]; other site 159087010416 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 159087010417 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 159087010418 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 159087010419 dimerization interface [polypeptide binding]; other site 159087010420 putative ATP binding site [chemical binding]; other site 159087010421 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 159087010422 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 159087010423 active site 159087010424 HIGH motif; other site 159087010425 dimer interface [polypeptide binding]; other site 159087010426 KMSKS motif; other site 159087010427 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 159087010428 RNA binding surface [nucleotide binding]; other site 159087010429 DNA-binding response regulator CreB; Provisional; Region: PRK11083 159087010430 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 159087010431 active site 159087010432 phosphorylation site [posttranslational modification] 159087010433 intermolecular recognition site; other site 159087010434 dimerization interface [polypeptide binding]; other site 159087010435 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 159087010436 DNA binding site [nucleotide binding] 159087010437 sensory histidine kinase CreC; Provisional; Region: PRK11100 159087010438 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 159087010439 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 159087010440 dimer interface [polypeptide binding]; other site 159087010441 phosphorylation site [posttranslational modification] 159087010442 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 159087010443 ATP binding site [chemical binding]; other site 159087010444 Mg2+ binding site [ion binding]; other site 159087010445 G-X-G motif; other site 159087010446 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 159087010447 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 159087010448 S-adenosylmethionine binding site [chemical binding]; other site 159087010449 inner membrane protein; Provisional; Region: PRK11715 159087010450 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 159087010451 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 159087010452 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 159087010453 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 159087010454 poly(A) polymerase; Region: pcnB; TIGR01942 159087010455 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 159087010456 active site 159087010457 NTP binding site [chemical binding]; other site 159087010458 metal binding triad [ion binding]; metal-binding site 159087010459 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 159087010460 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 159087010461 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 159087010462 catalytic center binding site [active] 159087010463 ATP binding site [chemical binding]; other site 159087010464 Protein of unknown function, DUF486; Region: DUF486; pfam04342 159087010465 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 159087010466 oligomerization interface [polypeptide binding]; other site 159087010467 active site 159087010468 metal binding site [ion binding]; metal-binding site 159087010469 pantoate--beta-alanine ligase; Region: panC; TIGR00018 159087010470 Pantoate-beta-alanine ligase; Region: PanC; cd00560 159087010471 active site 159087010472 ATP-binding site [chemical binding]; other site 159087010473 pantoate-binding site; other site 159087010474 HXXH motif; other site 159087010475 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 159087010476 tetramerization interface [polypeptide binding]; other site 159087010477 active site 159087010478 LabA_like proteins; Region: LabA_like; cd06167 159087010479 putative metal binding site [ion binding]; other site 159087010480 Uncharacterized conserved protein [Function unknown]; Region: COG1432 159087010481 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cl14879 159087010482 Cytochrome c; Region: Cytochrom_C; pfam00034 159087010483 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 159087010484 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 159087010485 Putative water exit pathway; other site 159087010486 Binuclear center (active site) [active] 159087010487 K-pathway; other site 159087010488 Putative proton exit pathway; other site 159087010489 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 159087010490 Subunit I/III interface [polypeptide binding]; other site 159087010491 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; pfam03626 159087010492 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 159087010493 MoxR-like ATPases [General function prediction only]; Region: COG0714 159087010494 Walker A motif; other site 159087010495 ATP binding site [chemical binding]; other site 159087010496 Walker B motif; other site 159087010497 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 159087010498 Tic20-like protein; Region: Tic20; pfam09685 159087010499 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 159087010500 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087010501 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 159087010502 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 159087010503 metal ion-dependent adhesion site (MIDAS); other site 159087010504 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087010505 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 159087010506 ligand binding site [chemical binding]; other site 159087010507 flexible hinge region; other site 159087010508 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 159087010509 putative switch regulator; other site 159087010510 non-specific DNA interactions [nucleotide binding]; other site 159087010511 DNA binding site [nucleotide binding] 159087010512 sequence specific DNA binding site [nucleotide binding]; other site 159087010513 putative cAMP binding site [chemical binding]; other site 159087010514 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010515 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010516 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010517 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010518 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010519 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010520 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010521 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010522 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010523 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010524 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010525 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010526 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010527 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010528 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010529 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010530 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010531 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010532 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010533 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010534 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010535 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010536 VCBS repeat; Region: VCBS_repeat; TIGR01965 159087010537 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 159087010538 metal ion-dependent adhesion site (MIDAS); other site 159087010539 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 159087010540 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 159087010541 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 159087010542 DNA binding residues [nucleotide binding] 159087010543 dimerization interface [polypeptide binding]; other site 159087010544 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 159087010545 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087010546 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 159087010547 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 159087010548 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 159087010549 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 159087010550 Walker A/P-loop; other site 159087010551 ATP binding site [chemical binding]; other site 159087010552 Q-loop/lid; other site 159087010553 ABC transporter signature motif; other site 159087010554 Walker B; other site 159087010555 D-loop; other site 159087010556 H-loop/switch region; other site 159087010557 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 159087010558 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 159087010559 6-phosphofructokinase; Provisional; Region: PRK14072 159087010560 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 159087010561 active site 159087010562 ADP/pyrophosphate binding site [chemical binding]; other site 159087010563 dimerization interface [polypeptide binding]; other site 159087010564 allosteric effector site; other site 159087010565 fructose-1,6-bisphosphate binding site; other site 159087010566 adenylate kinase; Reviewed; Region: adk; PRK00279 159087010567 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 159087010568 AMP-binding site [chemical binding]; other site 159087010569 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 159087010570 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 159087010571 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 159087010572 Ligand binding site; other site 159087010573 oligomer interface; other site 159087010574 Uncharacterized conserved protein [Function unknown]; Region: COG2835 159087010575 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 159087010576 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 159087010577 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 159087010578 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 159087010579 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 159087010580 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 159087010581 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 159087010582 generic binding surface II; other site 159087010583 generic binding surface I; other site 159087010584 superoxide dismutase; Provisional; Region: PRK10543 159087010585 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 159087010586 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 159087010587 Predicted membrane protein [Function unknown]; Region: COG2860 159087010588 UPF0126 domain; Region: UPF0126; pfam03458 159087010589 UPF0126 domain; Region: UPF0126; pfam03458 159087010590 YcaO domain protein; Region: TIGR03549 159087010591 OsmC-like protein; Region: OsmC; pfam02566 159087010592 YcaO-like family; Region: YcaO; pfam02624 159087010593 Domain of unknown function DUF21; Region: DUF21; pfam01595 159087010594 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 159087010595 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 159087010596 Transporter associated domain; Region: CorC_HlyC; smart01091 159087010597 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 159087010598 Secretin and TonB N terminus short domain; Region: STN; smart00965 159087010599 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 159087010600 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087010601 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 159087010602 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 159087010603 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 159087010604 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 159087010605 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 159087010606 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 159087010607 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 159087010608 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087010609 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 159087010610 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 159087010611 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087010612 catalytic residue [active] 159087010613 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 159087010614 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 159087010615 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 159087010616 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 159087010617 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 159087010618 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 159087010619 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 159087010620 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 159087010621 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 159087010622 Walker A motif; other site 159087010623 ATP binding site [chemical binding]; other site 159087010624 Walker B motif; other site 159087010625 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 159087010626 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 159087010627 dimer interface [polypeptide binding]; other site 159087010628 Alkaline phosphatase homologues; Region: alkPPc; smart00098 159087010629 active site 159087010630 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 159087010631 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 159087010632 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 159087010633 catalytic site [active] 159087010634 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 159087010635 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 159087010636 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 159087010637 CoenzymeA binding site [chemical binding]; other site 159087010638 subunit interaction site [polypeptide binding]; other site 159087010639 PHB binding site; other site 159087010640 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 159087010641 CoenzymeA binding site [chemical binding]; other site 159087010642 subunit interaction site [polypeptide binding]; other site 159087010643 PHB binding site; other site 159087010644 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087010645 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087010646 Walker A/P-loop; other site 159087010647 ATP binding site [chemical binding]; other site 159087010648 Q-loop/lid; other site 159087010649 ABC transporter signature motif; other site 159087010650 Walker B; other site 159087010651 D-loop; other site 159087010652 H-loop/switch region; other site 159087010653 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087010654 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087010655 TM-ABC transporter signature motif; other site 159087010656 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087010657 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087010658 Walker A/P-loop; other site 159087010659 ATP binding site [chemical binding]; other site 159087010660 Q-loop/lid; other site 159087010661 ABC transporter signature motif; other site 159087010662 Walker B; other site 159087010663 D-loop; other site 159087010664 H-loop/switch region; other site 159087010665 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087010666 TM-ABC transporter signature motif; other site 159087010667 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087010668 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 159087010669 catalytic loop [active] 159087010670 iron binding site [ion binding]; other site 159087010671 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 159087010672 FAD binding pocket [chemical binding]; other site 159087010673 FAD binding motif [chemical binding]; other site 159087010674 phosphate binding motif [ion binding]; other site 159087010675 beta-alpha-beta structure motif; other site 159087010676 NAD binding pocket [chemical binding]; other site 159087010677 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087010678 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087010679 active site 159087010680 catalytic residues [active] 159087010681 metal binding site [ion binding]; metal-binding site 159087010682 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087010683 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087010684 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 159087010685 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087010686 feruloyl-CoA synthase; Reviewed; Region: PRK08180 159087010687 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 159087010688 acyl-activating enzyme (AAE) consensus motif; other site 159087010689 putative AMP binding site [chemical binding]; other site 159087010690 putative active site [active] 159087010691 putative CoA binding site [chemical binding]; other site 159087010692 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087010693 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087010694 putative ligand binding site [chemical binding]; other site 159087010695 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087010696 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 159087010697 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 159087010698 FMN binding site [chemical binding]; other site 159087010699 substrate binding site [chemical binding]; other site 159087010700 putative catalytic residue [active] 159087010701 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional; Region: PRK06200 159087010702 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087010703 NAD(P) binding site [chemical binding]; other site 159087010704 active site 159087010705 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 159087010706 inter-subunit interface; other site 159087010707 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 159087010708 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 159087010709 iron-sulfur cluster [ion binding]; other site 159087010710 [2Fe-2S] cluster binding site [ion binding]; other site 159087010711 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 159087010712 beta subunit interface [polypeptide binding]; other site 159087010713 alpha subunit interface [polypeptide binding]; other site 159087010714 active site 159087010715 substrate binding site [chemical binding]; other site 159087010716 Fe binding site [ion binding]; other site 159087010717 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 159087010718 [2Fe-2S] cluster binding site [ion binding]; other site 159087010719 PhnC is a Class III Extradiol ring-cleavage dioxygenase involved in the polycyclic aromatic hydrocarbon (PAH) catabolic pathway; Region: PhnC_Bs_like; cd07368 159087010720 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 159087010721 putative active site [active] 159087010722 Fe(II) binding site [ion binding]; other site 159087010723 putative dimer interface [polypeptide binding]; other site 159087010724 putative tetramer interface [polypeptide binding]; other site 159087010725 Subunit A of Class III extradiol dioxygenases; Region: Extradiol_Dioxygenase_3A_like; cd07321 159087010726 dimer interface [polypeptide binding]; other site 159087010727 tetramer interface [polypeptide binding]; other site 159087010728 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087010729 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 159087010730 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087010731 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087010732 Chorismate lyase; Region: Chor_lyase; cl01230 159087010733 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 159087010734 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 159087010735 pseudouridine synthase; Region: TIGR00093 159087010736 active site 159087010737 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 159087010738 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 159087010739 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3786 159087010740 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 159087010741 Serine hydrolase (FSH1); Region: FSH1; pfam03959 159087010742 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087010743 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 159087010744 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 159087010745 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 159087010746 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 159087010747 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 159087010748 FeS/SAM binding site; other site 159087010749 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 159087010750 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 159087010751 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 159087010752 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 159087010753 Walker A/P-loop; other site 159087010754 ATP binding site [chemical binding]; other site 159087010755 Q-loop/lid; other site 159087010756 ABC transporter signature motif; other site 159087010757 Walker B; other site 159087010758 D-loop; other site 159087010759 H-loop/switch region; other site 159087010760 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 159087010761 cyanophycin synthetase; Provisional; Region: PRK14016 159087010762 ATP-grasp domain; Region: ATP-grasp_4; cl17255 159087010763 cyanophycin synthetase; Provisional; Region: PRK14016 159087010764 ATP-grasp domain; Region: ATP-grasp_4; cl17255 159087010765 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 159087010766 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087010767 ferredoxin-NADP reductase; Provisional; Region: PRK10926 159087010768 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 159087010769 FAD binding pocket [chemical binding]; other site 159087010770 FAD binding motif [chemical binding]; other site 159087010771 phosphate binding motif [ion binding]; other site 159087010772 beta-alpha-beta structure motif; other site 159087010773 NAD binding pocket [chemical binding]; other site 159087010774 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 159087010775 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 159087010776 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 159087010777 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 159087010778 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 159087010779 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 159087010780 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 159087010781 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 159087010782 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087010783 Plastocyanin [Energy production and conversion]; Region: PetE; COG3794 159087010784 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 159087010785 Domon-like ligand-binding domains; Region: DOMON_like; cd00241 159087010786 putative ligand binding site [chemical binding]; other site 159087010787 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087010788 Cytochrome c; Region: Cytochrom_C; pfam00034 159087010789 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 159087010790 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 159087010791 active site 159087010792 SAM binding site [chemical binding]; other site 159087010793 homodimer interface [polypeptide binding]; other site 159087010794 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 159087010795 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 159087010796 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 159087010797 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 159087010798 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 159087010799 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 159087010800 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 159087010801 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 159087010802 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 159087010803 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 159087010804 Protein export membrane protein; Region: SecD_SecF; pfam02355 159087010805 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 159087010806 Cytochrome C' Region: Cytochrom_C_2; pfam01322 159087010807 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087010808 PAS domain; Region: PAS; smart00091 159087010809 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087010810 putative active site [active] 159087010811 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087010812 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 159087010813 dimer interface [polypeptide binding]; other site 159087010814 phosphorylation site [posttranslational modification] 159087010815 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 159087010816 ATP binding site [chemical binding]; other site 159087010817 Mg2+ binding site [ion binding]; other site 159087010818 G-X-G motif; other site 159087010819 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087010820 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 159087010821 active site 159087010822 phosphorylation site [posttranslational modification] 159087010823 intermolecular recognition site; other site 159087010824 dimerization interface [polypeptide binding]; other site 159087010825 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087010826 Zn2+ binding site [ion binding]; other site 159087010827 Mg2+ binding site [ion binding]; other site 159087010828 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; pfam10084 159087010829 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 159087010830 adenylosuccinate lyase; Provisional; Region: PRK09285 159087010831 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 159087010832 tetramer interface [polypeptide binding]; other site 159087010833 active site 159087010834 putative glutathione S-transferase; Provisional; Region: PRK10357 159087010835 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 159087010836 putative C-terminal domain interface [polypeptide binding]; other site 159087010837 putative GSH binding site (G-site) [chemical binding]; other site 159087010838 putative dimer interface [polypeptide binding]; other site 159087010839 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 159087010840 dimer interface [polypeptide binding]; other site 159087010841 N-terminal domain interface [polypeptide binding]; other site 159087010842 putative substrate binding pocket (H-site) [chemical binding]; other site 159087010843 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 159087010844 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087010845 Zn2+ binding site [ion binding]; other site 159087010846 Mg2+ binding site [ion binding]; other site 159087010847 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 159087010848 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 159087010849 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 159087010850 nudix motif; other site 159087010851 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 159087010852 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 159087010853 homodimer interface [polypeptide binding]; other site 159087010854 substrate-cofactor binding pocket; other site 159087010855 catalytic residue [active] 159087010856 Zinc-finger domain; Region: zf-CHCC; cl01821 159087010857 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087010858 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 159087010859 putative active site [active] 159087010860 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 159087010861 SnoaL-like domain; Region: SnoaL_3; pfam13474 159087010862 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 159087010863 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 159087010864 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 159087010865 active site 159087010866 substrate binding site [chemical binding]; other site 159087010867 metal binding site [ion binding]; metal-binding site 159087010868 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 159087010869 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 159087010870 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 159087010871 motif 1; other site 159087010872 active site 159087010873 motif 2; other site 159087010874 motif 3; other site 159087010875 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 159087010876 DHHA1 domain; Region: DHHA1; pfam02272 159087010877 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 159087010878 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 159087010879 putative active site [active] 159087010880 catalytic site [active] 159087010881 putative metal binding site [ion binding]; other site 159087010882 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 159087010883 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 159087010884 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087010885 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 159087010886 dimerization interface [polypeptide binding]; other site 159087010887 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 159087010888 dimer interface [polypeptide binding]; other site 159087010889 phosphorylation site [posttranslational modification] 159087010890 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 159087010891 ATP binding site [chemical binding]; other site 159087010892 Mg2+ binding site [ion binding]; other site 159087010893 G-X-G motif; other site 159087010894 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 159087010895 Response regulator receiver domain; Region: Response_reg; pfam00072 159087010896 active site 159087010897 phosphorylation site [posttranslational modification] 159087010898 intermolecular recognition site; other site 159087010899 dimerization interface [polypeptide binding]; other site 159087010900 helicase 45; Provisional; Region: PTZ00424 159087010901 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 159087010902 ATP binding site [chemical binding]; other site 159087010903 Mg++ binding site [ion binding]; other site 159087010904 motif III; other site 159087010905 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 159087010906 nucleotide binding region [chemical binding]; other site 159087010907 ATP-binding site [chemical binding]; other site 159087010908 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087010909 active site 159087010910 HDOD domain; Region: HDOD; pfam08668 159087010911 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087010912 Zn2+ binding site [ion binding]; other site 159087010913 Mg2+ binding site [ion binding]; other site 159087010914 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 159087010915 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 159087010916 Cysteine-rich domain; Region: CCG; pfam02754 159087010917 Cysteine-rich domain; Region: CCG; pfam02754 159087010918 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 159087010919 FAD binding domain; Region: FAD_binding_4; pfam01565 159087010920 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 159087010921 FAD binding domain; Region: FAD_binding_4; pfam01565 159087010922 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 159087010923 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 159087010924 enoyl-CoA hydratase; Provisional; Region: PRK06142 159087010925 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 159087010926 substrate binding site [chemical binding]; other site 159087010927 oxyanion hole (OAH) forming residues; other site 159087010928 trimer interface [polypeptide binding]; other site 159087010929 Cytochrome c; Region: Cytochrom_C; cl11414 159087010930 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087010931 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 159087010932 ligand binding site [chemical binding]; other site 159087010933 flexible hinge region; other site 159087010934 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 159087010935 non-specific DNA interactions [nucleotide binding]; other site 159087010936 DNA binding site [nucleotide binding] 159087010937 sequence specific DNA binding site [nucleotide binding]; other site 159087010938 putative cAMP binding site [chemical binding]; other site 159087010939 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087010940 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087010941 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087010942 Cytochrome c; Region: Cytochrom_C; pfam00034 159087010943 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 159087010944 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 159087010945 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 159087010946 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 159087010947 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 159087010948 FeS/SAM binding site; other site 159087010949 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087010950 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087010951 Cytochrome c553 [Energy production and conversion]; Region: COG2863 159087010952 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087010953 Cytochrome c; Region: Cytochrom_C; cl11414 159087010954 protease TldD; Provisional; Region: tldD; PRK10735 159087010955 nitrilase; Region: PLN02798 159087010956 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 159087010957 putative active site [active] 159087010958 catalytic triad [active] 159087010959 dimer interface [polypeptide binding]; other site 159087010960 TIGR02099 family protein; Region: TIGR02099 159087010961 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 159087010962 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 159087010963 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087010964 metal binding triad; other site 159087010965 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 159087010966 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 159087010967 metal binding triad; other site 159087010968 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 159087010969 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 159087010970 methionine aminotransferase; Validated; Region: PRK09082 159087010971 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 159087010972 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087010973 homodimer interface [polypeptide binding]; other site 159087010974 catalytic residue [active] 159087010975 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 159087010976 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 159087010977 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 159087010978 intersubunit interface [polypeptide binding]; other site 159087010979 active site 159087010980 Zn2+ binding site [ion binding]; other site 159087010981 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 159087010982 Flagellar regulator YcgR; Region: YcgR; pfam07317 159087010983 PilZ domain; Region: PilZ; pfam07238 159087010984 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 159087010985 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 159087010986 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 159087010987 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 159087010988 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 159087010989 PAS domain; Region: PAS_9; pfam13426 159087010990 putative active site [active] 159087010991 heme pocket [chemical binding]; other site 159087010992 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087010993 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087010994 metal binding site [ion binding]; metal-binding site 159087010995 active site 159087010996 I-site; other site 159087010997 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 159087010998 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 159087010999 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 159087011000 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087011001 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087011002 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087011003 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 159087011004 Major Facilitator Superfamily; Region: MFS_1; pfam07690 159087011005 putative substrate translocation pore; other site 159087011006 Cytochrome c; Region: Cytochrom_C; cl11414 159087011007 Ion channel; Region: Ion_trans_2; pfam07885 159087011008 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 159087011009 TrkA-N domain; Region: TrkA_N; pfam02254 159087011010 Protein of unknown function (DUF3124); Region: DUF3124; pfam11322 159087011011 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011012 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 159087011013 active site 159087011014 phosphorylation site [posttranslational modification] 159087011015 intermolecular recognition site; other site 159087011016 dimerization interface [polypeptide binding]; other site 159087011017 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087011018 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 159087011019 dimerization interface [polypeptide binding]; other site 159087011020 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 159087011021 dimer interface [polypeptide binding]; other site 159087011022 phosphorylation site [posttranslational modification] 159087011023 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 159087011024 ATP binding site [chemical binding]; other site 159087011025 Mg2+ binding site [ion binding]; other site 159087011026 G-X-G motif; other site 159087011027 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087011028 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 159087011029 active site 159087011030 phosphorylation site [posttranslational modification] 159087011031 intermolecular recognition site; other site 159087011032 dimerization interface [polypeptide binding]; other site 159087011033 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011034 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 159087011035 active site 159087011036 phosphorylation site [posttranslational modification] 159087011037 intermolecular recognition site; other site 159087011038 dimerization interface [polypeptide binding]; other site 159087011039 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 159087011040 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 159087011041 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 159087011042 active site 159087011043 phosphorylation site [posttranslational modification] 159087011044 intermolecular recognition site; other site 159087011045 dimerization interface [polypeptide binding]; other site 159087011046 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 159087011047 DNA binding site [nucleotide binding] 159087011048 Predicted transglutaminase-like cysteine proteinase [General function prediction only]; Region: COG3672 159087011049 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 159087011050 HAMP domain; Region: HAMP; pfam00672 159087011051 dimerization interface [polypeptide binding]; other site 159087011052 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087011053 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011054 metal binding site [ion binding]; metal-binding site 159087011055 active site 159087011056 I-site; other site 159087011057 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 159087011058 Uncharacterized conserved protein [Function unknown]; Region: COG3025 159087011059 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 159087011060 putative active site [active] 159087011061 putative metal binding residues [ion binding]; other site 159087011062 signature motif; other site 159087011063 putative triphosphate binding site [ion binding]; other site 159087011064 The CHAD domain is an alpha-helical domain functionally associated with some members of the adenylate cyclase family; Region: CHAD; smart00880 159087011065 Pilin (bacterial filament); Region: Pilin; pfam00114 159087011066 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087011067 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 159087011068 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087011069 Zn2+ binding site [ion binding]; other site 159087011070 Mg2+ binding site [ion binding]; other site 159087011071 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087011072 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 159087011073 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 159087011074 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 159087011075 phosphopeptide binding site; other site 159087011076 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087011077 Protein phosphatase 2C; Region: PP2C; pfam00481 159087011078 active site 159087011079 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 159087011080 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 159087011081 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 159087011082 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 159087011083 CoA binding domain; Region: CoA_binding; smart00881 159087011084 CoA-ligase; Region: Ligase_CoA; pfam00549 159087011085 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 159087011086 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 159087011087 CoA-ligase; Region: Ligase_CoA; pfam00549 159087011088 multidrug efflux protein; Reviewed; Region: PRK01766 159087011089 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 159087011090 cation binding site [ion binding]; other site 159087011091 Phenylacetate-CoA ligase (also known as PaaK); Region: PaaK; cd05913 159087011092 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 159087011093 active site 159087011094 AMP binding site [chemical binding]; other site 159087011095 homodimer interface [polypeptide binding]; other site 159087011096 acyl-activating enzyme (AAE) consensus motif; other site 159087011097 CoA binding site [chemical binding]; other site 159087011098 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 159087011099 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 159087011100 FimV N-terminal domain; Region: FimV_core; TIGR03505 159087011101 Uncharacterized conserved protein [Function unknown]; Region: COG0327 159087011102 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 159087011103 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 159087011104 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 159087011105 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 159087011106 protein binding site [polypeptide binding]; other site 159087011107 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 159087011108 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 159087011109 putative active site [active] 159087011110 putative dimer interface [polypeptide binding]; other site 159087011111 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 159087011112 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 159087011113 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 159087011114 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 159087011115 nucleotide binding site/active site [active] 159087011116 HIT family signature motif; other site 159087011117 catalytic residue [active] 159087011118 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 159087011119 metal binding site [ion binding]; metal-binding site 159087011120 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 159087011121 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 159087011122 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 159087011123 substrate binding site [chemical binding]; other site 159087011124 glutamase interaction surface [polypeptide binding]; other site 159087011125 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 159087011126 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 159087011127 catalytic residues [active] 159087011128 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 159087011129 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 159087011130 putative active site [active] 159087011131 oxyanion strand; other site 159087011132 catalytic triad [active] 159087011133 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 159087011134 putative active site pocket [active] 159087011135 4-fold oligomerization interface [polypeptide binding]; other site 159087011136 metal binding residues [ion binding]; metal-binding site 159087011137 3-fold/trimer interface [polypeptide binding]; other site 159087011138 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 159087011139 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 159087011140 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087011141 homodimer interface [polypeptide binding]; other site 159087011142 catalytic residue [active] 159087011143 Chromate transporter; Region: Chromate_transp; pfam02417 159087011144 Chromate transporter; Region: Chromate_transp; pfam02417 159087011145 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 159087011146 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 159087011147 NAD binding site [chemical binding]; other site 159087011148 dimerization interface [polypeptide binding]; other site 159087011149 product binding site; other site 159087011150 substrate binding site [chemical binding]; other site 159087011151 zinc binding site [ion binding]; other site 159087011152 catalytic residues [active] 159087011153 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 159087011154 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 159087011155 DctM-like transporters; Region: DctM; pfam06808 159087011156 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 159087011157 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 159087011158 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 159087011159 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 159087011160 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 159087011161 DNA-binding site [nucleotide binding]; DNA binding site 159087011162 RNA-binding motif; other site 159087011163 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 159087011164 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 159087011165 hinge; other site 159087011166 active site 159087011167 BolA-like protein; Region: BolA; cl00386 159087011168 ABC-2 type transporter; Region: ABC2_membrane; cl17235 159087011169 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 159087011170 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 159087011171 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 159087011172 Walker A/P-loop; other site 159087011173 ATP binding site [chemical binding]; other site 159087011174 Q-loop/lid; other site 159087011175 ABC transporter signature motif; other site 159087011176 Walker B; other site 159087011177 D-loop; other site 159087011178 H-loop/switch region; other site 159087011179 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 159087011180 anti sigma factor interaction site; other site 159087011181 regulatory phosphorylation site [posttranslational modification]; other site 159087011182 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 159087011183 VacJ like lipoprotein; Region: VacJ; cl01073 159087011184 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 159087011185 mce related protein; Region: MCE; pfam02470 159087011186 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 159087011187 Permease; Region: Permease; pfam02405 159087011188 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 159087011189 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 159087011190 Walker A/P-loop; other site 159087011191 ATP binding site [chemical binding]; other site 159087011192 Q-loop/lid; other site 159087011193 ABC transporter signature motif; other site 159087011194 Walker B; other site 159087011195 D-loop; other site 159087011196 H-loop/switch region; other site 159087011197 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 159087011198 active site 159087011199 phosphorylation site [posttranslational modification] 159087011200 intermolecular recognition site; other site 159087011201 dimerization interface [polypeptide binding]; other site 159087011202 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 159087011203 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 159087011204 Walker A motif; other site 159087011205 ATP binding site [chemical binding]; other site 159087011206 Walker B motif; other site 159087011207 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087011208 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 159087011209 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 159087011210 Walker A motif; other site 159087011211 ATP binding site [chemical binding]; other site 159087011212 Walker B motif; other site 159087011213 arginine finger; other site 159087011214 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 159087011215 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 159087011216 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 159087011217 Tetratricopeptide repeat; Region: TPR_16; pfam13432 159087011218 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 159087011219 TPR motif; other site 159087011220 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 159087011221 TPR repeat; Region: TPR_11; pfam13414 159087011222 binding surface 159087011223 TPR motif; other site 159087011224 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 159087011225 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 159087011226 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 159087011227 Walker A motif; other site 159087011228 ATP binding site [chemical binding]; other site 159087011229 Walker B motif; other site 159087011230 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 159087011231 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 159087011232 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 159087011233 Heme NO binding associated; Region: HNOBA; pfam07701 159087011234 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 159087011235 cyclase homology domain; Region: CHD; cd07302 159087011236 nucleotidyl binding site; other site 159087011237 metal binding site [ion binding]; metal-binding site 159087011238 dimer interface [polypeptide binding]; other site 159087011239 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087011240 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; cl00075 159087011241 ATP binding site [chemical binding]; other site 159087011242 Mg2+ binding site [ion binding]; other site 159087011243 G-X-G motif; other site 159087011244 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 159087011245 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 159087011246 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 159087011247 TrkA-N domain; Region: TrkA_N; pfam02254 159087011248 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 159087011249 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 159087011250 putative active site [active] 159087011251 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 159087011252 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 159087011253 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 159087011254 active site 159087011255 motif I; other site 159087011256 motif II; other site 159087011257 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 159087011258 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 159087011259 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 159087011260 OstA-like protein; Region: OstA; pfam03968 159087011261 Phasin protein; Region: Phasin_2; pfam09361 159087011262 Phasin protein; Region: Phasin_2; pfam09361 159087011263 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 159087011264 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 159087011265 putative MPT binding site; other site 159087011266 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 159087011267 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 159087011268 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 159087011269 ATP binding site [chemical binding]; other site 159087011270 putative Mg++ binding site [ion binding]; other site 159087011271 helicase superfamily c-terminal domain; Region: HELICc; smart00490 159087011272 Helicase associated domain (HA2); Region: HA2; pfam04408 159087011273 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 159087011274 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 159087011275 integron integrase; Region: integrase_gron; TIGR02249 159087011276 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 159087011277 Int/Topo IB signature motif; other site 159087011278 DnaK-type molecular chaperone; Provisional; Region: PTZ00400 159087011279 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 159087011280 SseB protein; Region: SseB; cl06279 159087011281 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 159087011282 Transposase; Region: DEDD_Tnp_IS110; pfam01548 159087011283 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 159087011284 Domain of unknown function (DUF3601); Region: DUF3601; pfam12208 159087011285 Predicted integral membrane protein [Function unknown]; Region: COG3548 159087011286 putative acetyltransferase; Provisional; Region: PRK03624 159087011287 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087011288 Coenzyme A binding pocket [chemical binding]; other site 159087011289 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 159087011290 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 159087011291 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087011292 Coenzyme A binding pocket [chemical binding]; other site 159087011293 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 159087011294 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 159087011295 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 159087011296 DNA-binding site [nucleotide binding]; DNA binding site 159087011297 RNA-binding motif; other site 159087011298 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 159087011299 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 159087011300 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087011301 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 159087011302 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087011303 putative active site [active] 159087011304 heme pocket [chemical binding]; other site 159087011305 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 159087011306 putative active site [active] 159087011307 heme pocket [chemical binding]; other site 159087011308 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087011309 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 159087011310 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087011311 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011312 metal binding site [ion binding]; metal-binding site 159087011313 active site 159087011314 I-site; other site 159087011315 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 159087011316 chromosome condensation membrane protein; Provisional; Region: PRK14196 159087011317 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 159087011318 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087011319 active site 159087011320 HIGH motif; other site 159087011321 nucleotide binding site [chemical binding]; other site 159087011322 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087011323 active site 159087011324 KMSKS motif; other site 159087011325 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 159087011326 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 159087011327 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 159087011328 S-adenosylmethionine binding site [chemical binding]; other site 159087011329 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 159087011330 active site 159087011331 dimer interface [polypeptide binding]; other site 159087011332 Predicted metalloprotease [General function prediction only]; Region: COG2321 159087011333 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 159087011334 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 159087011335 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 159087011336 catalytic residues [active] 159087011337 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 159087011338 Peptidase family M23; Region: Peptidase_M23; pfam01551 159087011339 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 159087011340 homotrimer interaction site [polypeptide binding]; other site 159087011341 putative active site [active] 159087011342 PBP superfamily domain; Region: PBP_like_2; cl17296 159087011343 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087011344 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 159087011345 active site 159087011346 phosphorylation site [posttranslational modification] 159087011347 intermolecular recognition site; other site 159087011348 dimerization interface [polypeptide binding]; other site 159087011349 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087011350 Zn2+ binding site [ion binding]; other site 159087011351 Mg2+ binding site [ion binding]; other site 159087011352 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 159087011353 dimer interface [polypeptide binding]; other site 159087011354 phosphorylation site [posttranslational modification] 159087011355 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 159087011356 ATP binding site [chemical binding]; other site 159087011357 Mg2+ binding site [ion binding]; other site 159087011358 G-X-G motif; other site 159087011359 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 159087011360 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011361 active site 159087011362 phosphorylation site [posttranslational modification] 159087011363 intermolecular recognition site; other site 159087011364 dimerization interface [polypeptide binding]; other site 159087011365 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 159087011366 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011367 active site 159087011368 phosphorylation site [posttranslational modification] 159087011369 intermolecular recognition site; other site 159087011370 dimerization interface [polypeptide binding]; other site 159087011371 Hpt domain; Region: Hpt; pfam01627 159087011372 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087011373 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087011374 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087011375 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087011376 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 159087011377 Walker A/P-loop; other site 159087011378 ATP binding site [chemical binding]; other site 159087011379 Q-loop/lid; other site 159087011380 ABC transporter signature motif; other site 159087011381 Walker B; other site 159087011382 D-loop; other site 159087011383 H-loop/switch region; other site 159087011384 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087011385 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087011386 FtsX-like permease family; Region: FtsX; pfam02687 159087011387 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087011388 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087011389 FtsX-like permease family; Region: FtsX; pfam02687 159087011390 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 159087011391 dimer interaction site [polypeptide binding]; other site 159087011392 substrate-binding tunnel; other site 159087011393 active site 159087011394 catalytic site [active] 159087011395 substrate binding site [chemical binding]; other site 159087011396 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 159087011397 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 159087011398 RNA binding surface [nucleotide binding]; other site 159087011399 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 159087011400 active site 159087011401 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 159087011402 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 159087011403 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 159087011404 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 159087011405 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 159087011406 GTPase CgtA; Reviewed; Region: obgE; PRK12299 159087011407 GTP1/OBG; Region: GTP1_OBG; pfam01018 159087011408 Obg GTPase; Region: Obg; cd01898 159087011409 G1 box; other site 159087011410 GTP/Mg2+ binding site [chemical binding]; other site 159087011411 Switch I region; other site 159087011412 G2 box; other site 159087011413 G3 box; other site 159087011414 Switch II region; other site 159087011415 G4 box; other site 159087011416 G5 box; other site 159087011417 gamma-glutamyl kinase; Provisional; Region: PRK05429 159087011418 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 159087011419 nucleotide binding site [chemical binding]; other site 159087011420 homotetrameric interface [polypeptide binding]; other site 159087011421 putative phosphate binding site [ion binding]; other site 159087011422 putative allosteric binding site; other site 159087011423 PUA domain; Region: PUA; pfam01472 159087011424 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 159087011425 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 159087011426 trimer interface [polypeptide binding]; other site 159087011427 eyelet of channel; other site 159087011428 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 159087011429 active site 159087011430 ribulose/triose binding site [chemical binding]; other site 159087011431 phosphate binding site [ion binding]; other site 159087011432 substrate (anthranilate) binding pocket [chemical binding]; other site 159087011433 product (indole) binding pocket [chemical binding]; other site 159087011434 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 159087011435 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 159087011436 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 159087011437 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 159087011438 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 159087011439 glutamine binding [chemical binding]; other site 159087011440 catalytic triad [active] 159087011441 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 159087011442 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 159087011443 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 159087011444 active site 159087011445 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 159087011446 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 159087011447 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 159087011448 Ligand binding site; other site 159087011449 Putative Catalytic site; other site 159087011450 DXD motif; other site 159087011451 anthranilate synthase component I; Provisional; Region: PRK13565 159087011452 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 159087011453 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 159087011454 phosphoglycolate phosphatase; Provisional; Region: PRK13222 159087011455 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 159087011456 motif II; other site 159087011457 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 159087011458 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 159087011459 substrate binding site [chemical binding]; other site 159087011460 hexamer interface [polypeptide binding]; other site 159087011461 metal binding site [ion binding]; metal-binding site 159087011462 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 159087011463 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 159087011464 S-adenosylmethionine binding site [chemical binding]; other site 159087011465 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 159087011466 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 159087011467 heterotetramer interface [polypeptide binding]; other site 159087011468 active site pocket [active] 159087011469 cleavage site 159087011470 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 159087011471 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 159087011472 SEC-C motif; Region: SEC-C; pfam02810 159087011473 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 159087011474 Peptidase family M23; Region: Peptidase_M23; pfam01551 159087011475 Protein of unknown function (DUF721); Region: DUF721; pfam05258 159087011476 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 159087011477 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 159087011478 cell division protein FtsZ; Validated; Region: PRK09330 159087011479 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 159087011480 nucleotide binding site [chemical binding]; other site 159087011481 SulA interaction site; other site 159087011482 cell division protein FtsA; Region: ftsA; TIGR01174 159087011483 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 159087011484 nucleotide binding site [chemical binding]; other site 159087011485 Cell division protein FtsA; Region: FtsA; pfam14450 159087011486 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 159087011487 Cell division protein FtsQ; Region: FtsQ; pfam03799 159087011488 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 159087011489 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 159087011490 ATP-grasp domain; Region: ATP-grasp_4; cl17255 159087011491 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 159087011492 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 159087011493 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 159087011494 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087011495 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 159087011496 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 159087011497 active site 159087011498 homodimer interface [polypeptide binding]; other site 159087011499 cell division protein FtsW; Region: ftsW; TIGR02614 159087011500 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 159087011501 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 159087011502 NAD(P) binding pocket [chemical binding]; other site 159087011503 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 159087011504 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087011505 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 159087011506 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 159087011507 Mg++ binding site [ion binding]; other site 159087011508 putative catalytic motif [active] 159087011509 putative substrate binding site [chemical binding]; other site 159087011510 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 159087011511 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 159087011512 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 159087011513 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087011514 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 159087011515 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 159087011516 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 159087011517 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087011518 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 159087011519 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 159087011520 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 159087011521 Cell division protein FtsL; Region: FtsL; pfam04999 159087011522 MraW methylase family; Region: Methyltransf_5; pfam01795 159087011523 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 159087011524 cell division protein MraZ; Reviewed; Region: PRK00326 159087011525 MraZ protein; Region: MraZ; pfam02381 159087011526 MraZ protein; Region: MraZ; pfam02381 159087011527 Cache domain; Region: Cache_1; pfam02743 159087011528 PAS domain S-box; Region: sensory_box; TIGR00229 159087011529 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 159087011530 putative active site [active] 159087011531 heme pocket [chemical binding]; other site 159087011532 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087011533 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011534 metal binding site [ion binding]; metal-binding site 159087011535 active site 159087011536 I-site; other site 159087011537 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 159087011538 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 159087011539 dimerization domain [polypeptide binding]; other site 159087011540 dimer interface [polypeptide binding]; other site 159087011541 catalytic residues [active] 159087011542 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608 159087011543 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 159087011544 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 159087011545 IHF dimer interface [polypeptide binding]; other site 159087011546 IHF - DNA interface [nucleotide binding]; other site 159087011547 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 159087011548 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 159087011549 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 159087011550 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 159087011551 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 159087011552 [4Fe-4S] binding site [ion binding]; other site 159087011553 molybdopterin cofactor binding site; other site 159087011554 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 159087011555 molybdopterin cofactor binding site; other site 159087011556 NapD protein; Region: NapD; pfam03927 159087011557 peroxiredoxin; Region: AhpC; TIGR03137 159087011558 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 159087011559 dimer interface [polypeptide binding]; other site 159087011560 decamer (pentamer of dimers) interface [polypeptide binding]; other site 159087011561 catalytic triad [active] 159087011562 peroxidatic and resolving cysteines [active] 159087011563 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 159087011564 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 159087011565 catalytic residue [active] 159087011566 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 159087011567 catalytic residues [active] 159087011568 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 159087011569 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 159087011570 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 159087011571 Prophage antirepressor [Transcription]; Region: COG3617 159087011572 BRO family, N-terminal domain; Region: Bro-N; smart01040 159087011573 Protein of unknown function (DUF1376); Region: DUF1376; pfam07120 159087011574 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 159087011575 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 159087011576 catalytic residues [active] 159087011577 catalytic nucleophile [active] 159087011578 Presynaptic Site I dimer interface [polypeptide binding]; other site 159087011579 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 159087011580 Synaptic Flat tetramer interface [polypeptide binding]; other site 159087011581 Synaptic Site I dimer interface [polypeptide binding]; other site 159087011582 DNA binding site [nucleotide binding] 159087011583 Restriction endonuclease BglII; Region: Endonuc-BglII; pfam09195 159087011584 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 159087011585 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 159087011586 cofactor binding site; other site 159087011587 DNA binding site [nucleotide binding] 159087011588 substrate interaction site [chemical binding]; other site 159087011589 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 159087011590 active site 159087011591 Int/Topo IB signature motif; other site 159087011592 DNA binding site [nucleotide binding] 159087011593 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 159087011594 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 159087011595 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 159087011596 FeS/SAM binding site; other site 159087011597 TRAM domain; Region: TRAM; pfam01938 159087011598 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 159087011599 PhoH-like protein; Region: PhoH; pfam02562 159087011600 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 159087011601 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 159087011602 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 159087011603 Transporter associated domain; Region: CorC_HlyC; smart01091 159087011604 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 159087011605 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 159087011606 putative active site [active] 159087011607 catalytic triad [active] 159087011608 putative dimer interface [polypeptide binding]; other site 159087011609 methionine sulfoxide reductase A; Provisional; Region: PRK14054 159087011610 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 159087011611 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 159087011612 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087011613 catalytic residue [active] 159087011614 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 159087011615 dimer interface [polypeptide binding]; other site 159087011616 motif 1; other site 159087011617 active site 159087011618 motif 2; other site 159087011619 motif 3; other site 159087011620 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 159087011621 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 159087011622 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 159087011623 active site 159087011624 motif I; other site 159087011625 motif II; other site 159087011626 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 159087011627 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087011628 putative acyl-acceptor binding pocket; other site 159087011629 Protein of unknown function DUF45; Region: DUF45; pfam01863 159087011630 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 159087011631 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 159087011632 dimer interface [polypeptide binding]; other site 159087011633 active site 159087011634 metal binding site [ion binding]; metal-binding site 159087011635 glutathione binding site [chemical binding]; other site 159087011636 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087011637 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087011638 putative ligand binding site [chemical binding]; other site 159087011639 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 159087011640 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011641 active site 159087011642 phosphorylation site [posttranslational modification] 159087011643 intermolecular recognition site; other site 159087011644 dimerization interface [polypeptide binding]; other site 159087011645 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 159087011646 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 159087011647 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 159087011648 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087011649 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 159087011650 ligand binding site [chemical binding]; other site 159087011651 flexible hinge region; other site 159087011652 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 159087011653 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 159087011654 putative ADP-binding pocket [chemical binding]; other site 159087011655 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 159087011656 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 159087011657 putative active site [active] 159087011658 putative metal binding site [ion binding]; other site 159087011659 PAS domain S-box; Region: sensory_box; TIGR00229 159087011660 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 159087011661 putative active site [active] 159087011662 heme pocket [chemical binding]; other site 159087011663 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087011664 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 159087011665 putative active site [active] 159087011666 heme pocket [chemical binding]; other site 159087011667 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 159087011668 dimer interface [polypeptide binding]; other site 159087011669 phosphorylation site [posttranslational modification] 159087011670 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 159087011671 ATP binding site [chemical binding]; other site 159087011672 Mg2+ binding site [ion binding]; other site 159087011673 G-X-G motif; other site 159087011674 Response regulator receiver domain; Region: Response_reg; pfam00072 159087011675 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 159087011676 active site 159087011677 phosphorylation site [posttranslational modification] 159087011678 intermolecular recognition site; other site 159087011679 dimerization interface [polypeptide binding]; other site 159087011680 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 159087011681 active site 159087011682 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 159087011683 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 159087011684 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 159087011685 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 159087011686 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087011687 ATP-grasp domain; Region: ATP-grasp; pfam02222 159087011688 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 159087011689 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 159087011690 active site 159087011691 phosphorylation site [posttranslational modification] 159087011692 intermolecular recognition site; other site 159087011693 dimerization interface [polypeptide binding]; other site 159087011694 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087011695 Zn2+ binding site [ion binding]; other site 159087011696 Mg2+ binding site [ion binding]; other site 159087011697 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 159087011698 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 159087011699 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 159087011700 Chromate transporter; Region: Chromate_transp; pfam02417 159087011701 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 159087011702 potassium uptake protein; Region: kup; TIGR00794 159087011703 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 159087011704 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 159087011705 active site 159087011706 phosphorylation site [posttranslational modification] 159087011707 intermolecular recognition site; other site 159087011708 dimerization interface [polypeptide binding]; other site 159087011709 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 159087011710 DNA binding site [nucleotide binding] 159087011711 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 159087011712 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 159087011713 dimer interface [polypeptide binding]; other site 159087011714 phosphorylation site [posttranslational modification] 159087011715 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 159087011716 ATP binding site [chemical binding]; other site 159087011717 Mg2+ binding site [ion binding]; other site 159087011718 G-X-G motif; other site 159087011719 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 159087011720 tetramer (dimer of dimers) interface [polypeptide binding]; other site 159087011721 active site 159087011722 dimer interface [polypeptide binding]; other site 159087011723 phosphate binding protein; Region: ptsS_2; TIGR02136 159087011724 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 159087011725 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 159087011726 dimer interface [polypeptide binding]; other site 159087011727 conserved gate region; other site 159087011728 putative PBP binding loops; other site 159087011729 ABC-ATPase subunit interface; other site 159087011730 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 159087011731 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 159087011732 dimer interface [polypeptide binding]; other site 159087011733 conserved gate region; other site 159087011734 putative PBP binding loops; other site 159087011735 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 159087011736 ABC-ATPase subunit interface; other site 159087011737 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 159087011738 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 159087011739 Walker A/P-loop; other site 159087011740 ATP binding site [chemical binding]; other site 159087011741 Q-loop/lid; other site 159087011742 ABC transporter signature motif; other site 159087011743 Walker B; other site 159087011744 D-loop; other site 159087011745 H-loop/switch region; other site 159087011746 transcriptional regulator PhoU; Provisional; Region: PRK11115 159087011747 PhoU domain; Region: PhoU; pfam01895 159087011748 PhoU domain; Region: PhoU; pfam01895 159087011749 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 159087011750 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 159087011751 active site 159087011752 phosphorylation site [posttranslational modification] 159087011753 intermolecular recognition site; other site 159087011754 dimerization interface [polypeptide binding]; other site 159087011755 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 159087011756 DNA binding site [nucleotide binding] 159087011757 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 159087011758 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087011759 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 159087011760 putative active site [active] 159087011761 heme pocket [chemical binding]; other site 159087011762 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 159087011763 dimer interface [polypeptide binding]; other site 159087011764 phosphorylation site [posttranslational modification] 159087011765 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 159087011766 ATP binding site [chemical binding]; other site 159087011767 Mg2+ binding site [ion binding]; other site 159087011768 G-X-G motif; other site 159087011769 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 159087011770 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 159087011771 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 159087011772 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087011773 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087011774 Ankyrin repeat; Region: Ank; pfam00023 159087011775 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 159087011776 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 159087011777 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 159087011778 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 159087011779 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 159087011780 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087011781 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011782 metal binding site [ion binding]; metal-binding site 159087011783 active site 159087011784 I-site; other site 159087011785 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087011786 Coenzyme A binding pocket [chemical binding]; other site 159087011787 sensory histidine kinase CreC; Provisional; Region: PRK11100 159087011788 BON domain; Region: BON; pfam04972 159087011789 BON domain; Region: BON; pfam04972 159087011790 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 159087011791 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 159087011792 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087011793 dimer interface [polypeptide binding]; other site 159087011794 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 159087011795 putative CheW interface [polypeptide binding]; other site 159087011796 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 159087011797 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087011798 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 159087011799 dimerization interface [polypeptide binding]; other site 159087011800 substrate binding pocket [chemical binding]; other site 159087011801 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 159087011802 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 159087011803 putative substrate translocation pore; other site 159087011804 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 159087011805 CoenzymeA binding site [chemical binding]; other site 159087011806 subunit interaction site [polypeptide binding]; other site 159087011807 PHB binding site; other site 159087011808 oxidative damage protection protein; Provisional; Region: PRK05408 159087011809 N-acetylglutamate synthase; Validated; Region: PRK05279 159087011810 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 159087011811 putative feedback inhibition sensing region; other site 159087011812 putative nucleotide binding site [chemical binding]; other site 159087011813 putative substrate binding site [chemical binding]; other site 159087011814 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 159087011815 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087011816 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 159087011817 Coenzyme A binding pocket [chemical binding]; other site 159087011818 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 159087011819 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 159087011820 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 159087011821 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 159087011822 RNA methyltransferase, RsmE family; Region: TIGR00046 159087011823 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 159087011824 putative catalytic residue [active] 159087011825 PAS fold; Region: PAS_7; pfam12860 159087011826 PAS fold; Region: PAS_7; pfam12860 159087011827 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 159087011828 PAS domain; Region: PAS_9; pfam13426 159087011829 putative active site [active] 159087011830 heme pocket [chemical binding]; other site 159087011831 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087011832 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011833 metal binding site [ion binding]; metal-binding site 159087011834 active site 159087011835 I-site; other site 159087011836 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 159087011837 fructose-1,6-bisphosphatase family protein; Region: PLN02628 159087011838 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 159087011839 AMP binding site [chemical binding]; other site 159087011840 metal binding site [ion binding]; metal-binding site 159087011841 active site 159087011842 transketolase; Reviewed; Region: PRK12753 159087011843 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 159087011844 TPP-binding site [chemical binding]; other site 159087011845 dimer interface [polypeptide binding]; other site 159087011846 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 159087011847 PYR/PP interface [polypeptide binding]; other site 159087011848 dimer interface [polypeptide binding]; other site 159087011849 TPP binding site [chemical binding]; other site 159087011850 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 159087011851 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 159087011852 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 159087011853 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 159087011854 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 159087011855 erythrose-4-phosphate dehydrogenase; Region: E4PD_g-proteo; TIGR01532 159087011856 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 159087011857 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 159087011858 Phosphoglycerate kinase; Region: PGK; pfam00162 159087011859 substrate binding site [chemical binding]; other site 159087011860 hinge regions; other site 159087011861 ADP binding site [chemical binding]; other site 159087011862 catalytic site [active] 159087011863 pyruvate kinase; Provisional; Region: PRK05826 159087011864 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 159087011865 domain interfaces; other site 159087011866 active site 159087011867 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 159087011868 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 159087011869 intersubunit interface [polypeptide binding]; other site 159087011870 active site 159087011871 zinc binding site [ion binding]; other site 159087011872 Na+ binding site [ion binding]; other site 159087011873 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087011874 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087011875 ligand binding site [chemical binding]; other site 159087011876 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 159087011877 FOG: WD40 repeat [General function prediction only]; Region: COG2319 159087011878 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; cd00200 159087011879 structural tetrad; other site 159087011880 FOG: WD40 repeat [General function prediction only]; Region: COG2319 159087011881 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; cd00200 159087011882 structural tetrad; other site 159087011883 WD40 repeats; Region: WD40; smart00320 159087011884 TIR domain; Region: TIR_2; pfam13676 159087011885 Domain of unknown function (DUF4157); Region: DUF4157; pfam13699 159087011886 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 159087011887 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 159087011888 Walker A motif; other site 159087011889 ATP binding site [chemical binding]; other site 159087011890 Walker B motif; other site 159087011891 arginine finger; other site 159087011892 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 159087011893 metal ion-dependent adhesion site (MIDAS); other site 159087011894 conserved hypothetical protein, phage tail-like region; Region: TIGR02243 159087011895 Gene 25-like lysozyme; Region: GPW_gp25; pfam04965 159087011896 PAAR motif; Region: PAAR_motif; cl15808 159087011897 Phage protein D [General function prediction only]; Region: COG3500 159087011898 Rhs element Vgr protein; Region: vgr_GE; TIGR01646 159087011899 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 159087011900 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 159087011901 T4-like virus tail tube protein gp19; Region: Phage_T4_gp19; pfam06841 159087011902 T4-like virus tail tube protein gp19; Region: Phage_T4_gp19; pfam06841 159087011903 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 159087011904 Phage tail sheath protein FI [General function prediction only]; Region: COG3497 159087011905 Protein of unknown function (DUF4255); Region: DUF4255; pfam14065 159087011906 Caspase domain; Region: Peptidase_C14; pfam00656 159087011907 Putative serine esterase (DUF676); Region: DUF676; pfam05057 159087011908 CHAT domain; Region: CHAT; pfam12770 159087011909 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 159087011910 Peptidase M15; Region: Peptidase_M15_3; cl01194 159087011911 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087011912 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011913 metal binding site [ion binding]; metal-binding site 159087011914 active site 159087011915 I-site; other site 159087011916 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 159087011917 PAS fold; Region: PAS_4; pfam08448 159087011918 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 159087011919 putative active site [active] 159087011920 heme pocket [chemical binding]; other site 159087011921 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 159087011922 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 159087011923 putative active site [active] 159087011924 heme pocket [chemical binding]; other site 159087011925 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 159087011926 putative active site [active] 159087011927 heme pocket [chemical binding]; other site 159087011928 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087011929 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087011930 metal binding site [ion binding]; metal-binding site 159087011931 active site 159087011932 I-site; other site 159087011933 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 159087011934 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 159087011935 intersubunit interface [polypeptide binding]; other site 159087011936 active site 159087011937 zinc binding site [ion binding]; other site 159087011938 Na+ binding site [ion binding]; other site 159087011939 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 159087011940 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 159087011941 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 159087011942 transketolase; Reviewed; Region: PRK12753 159087011943 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 159087011944 TPP-binding site [chemical binding]; other site 159087011945 dimer interface [polypeptide binding]; other site 159087011946 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 159087011947 PYR/PP interface [polypeptide binding]; other site 159087011948 dimer interface [polypeptide binding]; other site 159087011949 TPP binding site [chemical binding]; other site 159087011950 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 159087011951 phosphoribulokinase; Provisional; Region: PRK15453 159087011952 active site 159087011953 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 159087011954 AMP binding site [chemical binding]; other site 159087011955 metal binding site [ion binding]; metal-binding site 159087011956 active site 159087011957 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 159087011958 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 159087011959 motif II; other site 159087011960 Predicted membrane protein [Function unknown]; Region: COG2860 159087011961 UPF0126 domain; Region: UPF0126; pfam03458 159087011962 UPF0126 domain; Region: UPF0126; pfam03458 159087011963 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 159087011964 HSP70 interaction site [polypeptide binding]; other site 159087011965 ribulose bisphosphate carboxylase; Provisional; Region: PRK13475 159087011966 Ribulose bisphosphate carboxylase large chain, Form II; Region: RuBisCO_large_II; cd08211 159087011967 dimer interface [polypeptide binding]; other site 159087011968 active site 159087011969 catalytic residue [active] 159087011970 metal binding site [ion binding]; metal-binding site 159087011971 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087011972 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087011973 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 159087011974 putative dimerization interface [polypeptide binding]; other site 159087011975 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 159087011976 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 159087011977 ATP binding site [chemical binding]; other site 159087011978 active site 159087011979 substrate binding site [chemical binding]; other site 159087011980 Protein of unknown function (DUF2743); Region: DUF2743; pfam10899 159087011981 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 159087011982 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 159087011983 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 159087011984 active site 159087011985 Zn binding site [ion binding]; other site 159087011986 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 159087011987 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 159087011988 catalytic residues [active] 159087011989 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 159087011990 putative catalytic site [active] 159087011991 putative phosphate binding site [ion binding]; other site 159087011992 active site 159087011993 metal binding site A [ion binding]; metal-binding site 159087011994 DNA binding site [nucleotide binding] 159087011995 putative AP binding site [nucleotide binding]; other site 159087011996 putative metal binding site B [ion binding]; other site 159087011997 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087011998 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 159087011999 ligand binding site [chemical binding]; other site 159087012000 flexible hinge region; other site 159087012001 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 159087012002 non-specific DNA interactions [nucleotide binding]; other site 159087012003 DNA binding site [nucleotide binding] 159087012004 sequence specific DNA binding site [nucleotide binding]; other site 159087012005 putative cAMP binding site [chemical binding]; other site 159087012006 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 159087012007 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 159087012008 multiple promoter invertase; Provisional; Region: mpi; PRK13413 159087012009 catalytic residues [active] 159087012010 catalytic nucleophile [active] 159087012011 Presynaptic Site I dimer interface [polypeptide binding]; other site 159087012012 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 159087012013 Synaptic Flat tetramer interface [polypeptide binding]; other site 159087012014 Synaptic Site I dimer interface [polypeptide binding]; other site 159087012015 DNA binding site [nucleotide binding] 159087012016 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 159087012017 DNA-binding interface [nucleotide binding]; DNA binding site 159087012018 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 159087012019 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 159087012020 Walker A motif; other site 159087012021 ATP binding site [chemical binding]; other site 159087012022 Walker B motif; other site 159087012023 arginine finger; other site 159087012024 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]; Region: COG4916 159087012025 TIR domain; Region: TIR_2; pfam13676 159087012026 integrase; Provisional; Region: int; PHA02601 159087012027 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 159087012028 active site 159087012029 DNA binding site [nucleotide binding] 159087012030 Int/Topo IB signature motif; other site 159087012031 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 159087012032 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 159087012033 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 159087012034 S-adenosylmethionine binding site [chemical binding]; other site 159087012035 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 159087012036 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 159087012037 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 159087012038 SurA N-terminal domain; Region: SurA_N; pfam09312 159087012039 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 159087012040 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 159087012041 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 159087012042 Organic solvent tolerance protein; Region: OstA_C; pfam04453 159087012043 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 159087012044 Phosphotransferase enzyme family; Region: APH; pfam01636 159087012045 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 159087012046 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 159087012047 Substrate binding site; other site 159087012048 metal-binding site 159087012049 proline aminopeptidase P II; Provisional; Region: PRK10879 159087012050 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 159087012051 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 159087012052 active site 159087012053 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 159087012054 hypothetical protein; Provisional; Region: PRK06996 159087012055 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 159087012056 UbiA prenyltransferase family; Region: UbiA; pfam01040 159087012057 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 159087012058 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 159087012059 FMN binding site [chemical binding]; other site 159087012060 active site 159087012061 catalytic residues [active] 159087012062 substrate binding site [chemical binding]; other site 159087012063 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 159087012064 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 159087012065 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 159087012066 purine monophosphate binding site [chemical binding]; other site 159087012067 dimer interface [polypeptide binding]; other site 159087012068 putative catalytic residues [active] 159087012069 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 159087012070 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 159087012071 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 159087012072 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 159087012073 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 159087012074 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 159087012075 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 159087012076 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 159087012077 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 159087012078 HemY protein N-terminus; Region: HemY_N; pfam07219 159087012079 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 159087012080 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 159087012081 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 159087012082 active site 159087012083 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 159087012084 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 159087012085 domain interfaces; other site 159087012086 active site 159087012087 Thiopurine S-methyltransferase (TPMT); Region: TPMT; pfam05724 159087012088 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 159087012089 S-adenosylmethionine binding site [chemical binding]; other site 159087012090 aminopeptidase N; Provisional; Region: pepN; PRK14015 159087012091 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 159087012092 active site 159087012093 Zn binding site [ion binding]; other site 159087012094 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 159087012095 RNA/DNA hybrid binding site [nucleotide binding]; other site 159087012096 active site 159087012097 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 159087012098 catalytic residues [active] 159087012099 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 159087012100 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 159087012101 active site 159087012102 phosphorylation site [posttranslational modification] 159087012103 intermolecular recognition site; other site 159087012104 dimerization interface [polypeptide binding]; other site 159087012105 LytTr DNA-binding domain; Region: LytTR; smart00850 159087012106 Histidine kinase; Region: His_kinase; pfam06580 159087012107 argininosuccinate lyase; Provisional; Region: PRK00855 159087012108 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 159087012109 active sites [active] 159087012110 tetramer interface [polypeptide binding]; other site 159087012111 OsmC-like protein; Region: OsmC; cl00767 159087012112 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 159087012113 putative GSH binding site [chemical binding]; other site 159087012114 catalytic residues [active] 159087012115 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 159087012116 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 159087012117 S-adenosylmethionine binding site [chemical binding]; other site 159087012118 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087012119 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087012120 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 159087012121 dimerization interface [polypeptide binding]; other site 159087012122 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 159087012123 dimer interface [polypeptide binding]; other site 159087012124 phosphorylation site [posttranslational modification] 159087012125 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 159087012126 ATP binding site [chemical binding]; other site 159087012127 Mg2+ binding site [ion binding]; other site 159087012128 G-X-G motif; other site 159087012129 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012130 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 159087012131 active site 159087012132 phosphorylation site [posttranslational modification] 159087012133 intermolecular recognition site; other site 159087012134 dimerization interface [polypeptide binding]; other site 159087012135 peptide chain release factor 1; Validated; Region: prfA; PRK00591 159087012136 This domain is found in peptide chain release factors; Region: PCRF; smart00937 159087012137 RF-1 domain; Region: RF-1; pfam00472 159087012138 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012139 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 159087012140 active site 159087012141 phosphorylation site [posttranslational modification] 159087012142 intermolecular recognition site; other site 159087012143 dimerization interface [polypeptide binding]; other site 159087012144 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087012145 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012146 metal binding site [ion binding]; metal-binding site 159087012147 active site 159087012148 I-site; other site 159087012149 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 159087012150 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 159087012151 tRNA; other site 159087012152 putative tRNA binding site [nucleotide binding]; other site 159087012153 putative NADP binding site [chemical binding]; other site 159087012154 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 159087012155 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 159087012156 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 159087012157 Walker A/P-loop; other site 159087012158 ATP binding site [chemical binding]; other site 159087012159 Q-loop/lid; other site 159087012160 ABC transporter signature motif; other site 159087012161 Walker B; other site 159087012162 D-loop; other site 159087012163 H-loop/switch region; other site 159087012164 TOBE-like domain; Region: TOBE_3; pfam12857 159087012165 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 159087012166 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 159087012167 dimer interface [polypeptide binding]; other site 159087012168 conserved gate region; other site 159087012169 putative PBP binding loops; other site 159087012170 ABC-ATPase subunit interface; other site 159087012171 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 159087012172 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 159087012173 dimer interface [polypeptide binding]; other site 159087012174 conserved gate region; other site 159087012175 putative PBP binding loops; other site 159087012176 ABC-ATPase subunit interface; other site 159087012177 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 159087012178 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 159087012179 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087012180 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087012181 ligand binding site [chemical binding]; other site 159087012182 Nitrate and nitrite sensing; Region: NIT; pfam08376 159087012183 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 159087012184 PAS domain; Region: PAS_9; pfam13426 159087012185 putative active site [active] 159087012186 heme pocket [chemical binding]; other site 159087012187 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087012188 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012189 metal binding site [ion binding]; metal-binding site 159087012190 active site 159087012191 I-site; other site 159087012192 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 159087012193 Hemerythrin; Region: Hemerythrin; cd12107 159087012194 Fe binding site [ion binding]; other site 159087012195 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 159087012196 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 159087012197 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 159087012198 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 159087012199 tetramer interface [polypeptide binding]; other site 159087012200 TPP-binding site [chemical binding]; other site 159087012201 heterodimer interface [polypeptide binding]; other site 159087012202 phosphorylation loop region [posttranslational modification] 159087012203 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 159087012204 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 159087012205 PYR/PP interface [polypeptide binding]; other site 159087012206 dimer interface [polypeptide binding]; other site 159087012207 TPP binding site [chemical binding]; other site 159087012208 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 159087012209 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 159087012210 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 159087012211 MltA specific insert domain; Region: MltA; smart00925 159087012212 3D domain; Region: 3D; pfam06725 159087012213 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 159087012214 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 159087012215 Walker A motif; other site 159087012216 ATP binding site [chemical binding]; other site 159087012217 Walker B motif; other site 159087012218 hypothetical protein; Provisional; Region: PRK08999 159087012219 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 159087012220 active site 159087012221 8-oxo-dGMP binding site [chemical binding]; other site 159087012222 nudix motif; other site 159087012223 metal binding site [ion binding]; metal-binding site 159087012224 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 159087012225 active site 159087012226 thiamine phosphate binding site [chemical binding]; other site 159087012227 pyrophosphate binding site [ion binding]; other site 159087012228 Domain of unknown function (DUF329); Region: DUF329; pfam03884 159087012229 hypothetical protein; Provisional; Region: PRK05287 159087012230 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 159087012231 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 159087012232 CoA-binding site [chemical binding]; other site 159087012233 ATP-binding [chemical binding]; other site 159087012234 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087012235 tryptophan synthase subunit beta; Reviewed; Region: PRK12391 159087012236 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 159087012237 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 159087012238 catalytic residue [active] 159087012239 Domon-like domain of UDP-N-acetylenolpyruvoylglucosamine reductase; Region: DOMON_murB_like; cd09627 159087012240 putative heme binding site [chemical binding]; other site 159087012241 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 159087012242 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087012243 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 159087012244 substrate binding pocket [chemical binding]; other site 159087012245 membrane-bound complex binding site; other site 159087012246 hinge residues; other site 159087012247 PAS domain S-box; Region: sensory_box; TIGR00229 159087012248 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 159087012249 putative active site [active] 159087012250 heme pocket [chemical binding]; other site 159087012251 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087012252 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 159087012253 putative active site [active] 159087012254 heme pocket [chemical binding]; other site 159087012255 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 159087012256 dimer interface [polypeptide binding]; other site 159087012257 phosphorylation site [posttranslational modification] 159087012258 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 159087012259 ATP binding site [chemical binding]; other site 159087012260 Mg2+ binding site [ion binding]; other site 159087012261 G-X-G motif; other site 159087012262 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012263 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 159087012264 active site 159087012265 phosphorylation site [posttranslational modification] 159087012266 intermolecular recognition site; other site 159087012267 dimerization interface [polypeptide binding]; other site 159087012268 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 159087012269 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 159087012270 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 159087012271 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 159087012272 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087012273 Walker A/P-loop; other site 159087012274 ATP binding site [chemical binding]; other site 159087012275 Q-loop/lid; other site 159087012276 ABC transporter signature motif; other site 159087012277 Walker B; other site 159087012278 D-loop; other site 159087012279 H-loop/switch region; other site 159087012280 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 159087012281 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 159087012282 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 159087012283 P loop; other site 159087012284 GTP binding site [chemical binding]; other site 159087012285 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 159087012286 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 159087012287 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 159087012288 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 159087012289 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 159087012290 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 159087012291 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 159087012292 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 159087012293 S-adenosylmethionine binding site [chemical binding]; other site 159087012294 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 159087012295 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 159087012296 active site 159087012297 (T/H)XGH motif; other site 159087012298 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087012299 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 159087012300 Dynamin family; Region: Dynamin_N; pfam00350 159087012301 G1 box; other site 159087012302 GTP/Mg2+ binding site [chemical binding]; other site 159087012303 G2 box; other site 159087012304 Switch I region; other site 159087012305 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 159087012306 G3 box; other site 159087012307 Switch II region; other site 159087012308 GTP/Mg2+ binding site [chemical binding]; other site 159087012309 G4 box; other site 159087012310 G5 box; other site 159087012311 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 159087012312 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 159087012313 DNA binding site [nucleotide binding] 159087012314 catalytic residue [active] 159087012315 H2TH interface [polypeptide binding]; other site 159087012316 putative catalytic residues [active] 159087012317 turnover-facilitating residue; other site 159087012318 intercalation triad [nucleotide binding]; other site 159087012319 8OG recognition residue [nucleotide binding]; other site 159087012320 putative reading head residues; other site 159087012321 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 159087012322 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 159087012323 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 159087012324 TPR motif; other site 159087012325 binding surface 159087012326 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 159087012327 binding surface 159087012328 TPR motif; other site 159087012329 TPR repeat; Region: TPR_11; pfam13414 159087012330 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 159087012331 binding surface 159087012332 TPR motif; other site 159087012333 TPR repeat; Region: TPR_11; pfam13414 159087012334 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 159087012335 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 159087012336 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 159087012337 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 159087012338 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 159087012339 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 159087012340 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 159087012341 active site 159087012342 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 159087012343 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 159087012344 5S rRNA interface [nucleotide binding]; other site 159087012345 CTC domain interface [polypeptide binding]; other site 159087012346 L16 interface [polypeptide binding]; other site 159087012347 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 159087012348 putative active site [active] 159087012349 catalytic residue [active] 159087012350 GTP-binding protein YchF; Reviewed; Region: PRK09601 159087012351 YchF GTPase; Region: YchF; cd01900 159087012352 G1 box; other site 159087012353 GTP/Mg2+ binding site [chemical binding]; other site 159087012354 Switch I region; other site 159087012355 G2 box; other site 159087012356 Switch II region; other site 159087012357 G3 box; other site 159087012358 G4 box; other site 159087012359 G5 box; other site 159087012360 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 159087012361 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 159087012362 PAS domain; Region: PAS_9; pfam13426 159087012363 putative active site [active] 159087012364 heme pocket [chemical binding]; other site 159087012365 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087012366 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012367 metal binding site [ion binding]; metal-binding site 159087012368 active site 159087012369 I-site; other site 159087012370 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 159087012371 spermidine synthase; Provisional; Region: PRK03612 159087012372 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 159087012373 Uncharacterized conserved protein [Function unknown]; Region: COG2353 159087012374 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 159087012375 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 159087012376 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 159087012377 dimerization interface [polypeptide binding]; other site 159087012378 active site 159087012379 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 159087012380 homopentamer interface [polypeptide binding]; other site 159087012381 active site 159087012382 transcription antitermination factor NusB; Region: nusB; TIGR01951 159087012383 thiamine monophosphate kinase; Provisional; Region: PRK05731 159087012384 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 159087012385 ATP binding site [chemical binding]; other site 159087012386 dimerization interface [polypeptide binding]; other site 159087012387 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 159087012388 tetramer interfaces [polypeptide binding]; other site 159087012389 binuclear metal-binding site [ion binding]; other site 159087012390 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012391 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 159087012392 active site 159087012393 phosphorylation site [posttranslational modification] 159087012394 intermolecular recognition site; other site 159087012395 dimerization interface [polypeptide binding]; other site 159087012396 PAS domain S-box; Region: sensory_box; TIGR00229 159087012397 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 159087012398 putative active site [active] 159087012399 heme pocket [chemical binding]; other site 159087012400 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087012401 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012402 metal binding site [ion binding]; metal-binding site 159087012403 active site 159087012404 I-site; other site 159087012405 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 159087012406 HDOD domain; Region: HDOD; pfam08668 159087012407 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087012408 Zn2+ binding site [ion binding]; other site 159087012409 Mg2+ binding site [ion binding]; other site 159087012410 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087012411 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 159087012412 ATP binding site [chemical binding]; other site 159087012413 Mg2+ binding site [ion binding]; other site 159087012414 G-X-G motif; other site 159087012415 choice-of-anchor C domain; Region: choice_anch_C; TIGR04362 159087012416 HDOD domain; Region: HDOD; pfam08668 159087012417 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 159087012418 NlpC/P60 family; Region: NLPC_P60; pfam00877 159087012419 succinic semialdehyde dehydrogenase; Region: PLN02278 159087012420 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 159087012421 tetramerization interface [polypeptide binding]; other site 159087012422 NAD(P) binding site [chemical binding]; other site 159087012423 catalytic residues [active] 159087012424 Uncharacterized conserved protein [Function unknown]; Region: COG4278 159087012425 NMT1/THI5 like; Region: NMT1; pfam09084 159087012426 PAS domain S-box; Region: sensory_box; TIGR00229 159087012427 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 159087012428 putative active site [active] 159087012429 heme pocket [chemical binding]; other site 159087012430 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087012431 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012432 metal binding site [ion binding]; metal-binding site 159087012433 active site 159087012434 I-site; other site 159087012435 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 159087012436 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 159087012437 Predicted membrane protein [Function unknown]; Region: COG3766 159087012438 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 159087012439 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 159087012440 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 159087012441 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 159087012442 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 159087012443 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 159087012444 Zn2+ binding site [ion binding]; other site 159087012445 Mg2+ binding site [ion binding]; other site 159087012446 pantothenate kinase; Reviewed; Region: PRK13329 159087012447 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 159087012448 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 159087012449 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 159087012450 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 159087012451 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 159087012452 active site 159087012453 phosphorylation site [posttranslational modification] 159087012454 intermolecular recognition site; other site 159087012455 dimerization interface [polypeptide binding]; other site 159087012456 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 159087012457 Walker A motif; other site 159087012458 ATP binding site [chemical binding]; other site 159087012459 Walker B motif; other site 159087012460 arginine finger; other site 159087012461 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087012462 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 159087012463 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 159087012464 putative active site [active] 159087012465 heme pocket [chemical binding]; other site 159087012466 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 159087012467 dimer interface [polypeptide binding]; other site 159087012468 phosphorylation site [posttranslational modification] 159087012469 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 159087012470 ATP binding site [chemical binding]; other site 159087012471 Mg2+ binding site [ion binding]; other site 159087012472 G-X-G motif; other site 159087012473 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087012474 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087012475 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 159087012476 glutamine synthetase; Provisional; Region: glnA; PRK09469 159087012477 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 159087012478 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 159087012479 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 159087012480 Cation efflux family; Region: Cation_efflux; pfam01545 159087012481 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 159087012482 active site residue [active] 159087012483 quinolinate synthetase; Provisional; Region: PRK09375 159087012484 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 159087012485 putative catalytic site [active] 159087012486 putative metal binding site [ion binding]; other site 159087012487 putative phosphate binding site [ion binding]; other site 159087012488 cardiolipin synthase 2; Provisional; Region: PRK11263 159087012489 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 159087012490 putative active site [active] 159087012491 catalytic site [active] 159087012492 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 159087012493 putative active site [active] 159087012494 catalytic site [active] 159087012495 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 159087012496 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 159087012497 active site 159087012498 HIGH motif; other site 159087012499 nucleotide binding site [chemical binding]; other site 159087012500 active site 159087012501 KMSKS motif; other site 159087012502 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 159087012503 PAS domain; Region: PAS_9; pfam13426 159087012504 putative active site [active] 159087012505 heme pocket [chemical binding]; other site 159087012506 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087012507 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012508 metal binding site [ion binding]; metal-binding site 159087012509 active site 159087012510 I-site; other site 159087012511 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 159087012512 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 159087012513 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 159087012514 catalytic residues [active] 159087012515 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 159087012516 tartrate dehydrogenase; Region: TTC; TIGR02089 159087012517 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 159087012518 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 159087012519 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 159087012520 VPS10 domain; Region: VPS10; smart00602 159087012521 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 159087012522 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 159087012523 active site 1 [active] 159087012524 dimer interface [polypeptide binding]; other site 159087012525 hexamer interface [polypeptide binding]; other site 159087012526 active site 2 [active] 159087012527 4-oxalocrotonate decarboxylase; Region: catechol_dmpH; TIGR03218 159087012528 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087012529 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087012530 active site 159087012531 catalytic residues [active] 159087012532 metal binding site [ion binding]; metal-binding site 159087012533 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087012534 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087012535 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 159087012536 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087012537 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 159087012538 classical (c) SDRs; Region: SDR_c; cd05233 159087012539 NAD(P) binding site [chemical binding]; other site 159087012540 active site 159087012541 2-oxopent-4-enoate hydratase; Region: catechol_dmpE; TIGR03220 159087012542 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 159087012543 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 159087012544 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 159087012545 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 159087012546 NAD binding site [chemical binding]; other site 159087012547 catalytic residues [active] 159087012548 Domain of unknown function (DUF336); Region: DUF336; pfam03928 159087012549 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 159087012550 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 159087012551 tetramer interface [polypeptide binding]; other site 159087012552 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 159087012553 tetramer interface [polypeptide binding]; other site 159087012554 active site 159087012555 Fe binding site [ion binding]; other site 159087012556 DNA-binding transcriptional regulator CsiR; Provisional; Region: PRK11534 159087012557 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087012558 DNA-binding site [nucleotide binding]; DNA binding site 159087012559 FCD domain; Region: FCD; pfam07729 159087012560 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 159087012561 catalytic loop [active] 159087012562 iron binding site [ion binding]; other site 159087012563 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087012564 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 159087012565 catalytic loop [active] 159087012566 iron binding site [ion binding]; other site 159087012567 Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H...; Region: phenol_2-monooxygenase_like; cd06211 159087012568 FAD binding pocket [chemical binding]; other site 159087012569 FAD binding motif [chemical binding]; other site 159087012570 phosphate binding motif [ion binding]; other site 159087012571 beta-alpha-beta structure motif; other site 159087012572 NAD binding pocket [chemical binding]; other site 159087012573 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 159087012574 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 159087012575 dimerization interface [polypeptide binding]; other site 159087012576 putative path to active site cavity [active] 159087012577 diiron center [ion binding]; other site 159087012578 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 159087012579 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 159087012580 dimerization interface [polypeptide binding]; other site 159087012581 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 159087012582 Activator of aromatic catabolism; Region: XylR_N; pfam06505 159087012583 V4R domain; Region: V4R; pfam02830 159087012584 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 159087012585 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 159087012586 Walker A motif; other site 159087012587 ATP binding site [chemical binding]; other site 159087012588 Walker B motif; other site 159087012589 arginine finger; other site 159087012590 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087012591 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087012592 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 159087012593 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; Region: PBP2_Chlorocatechol; cd08446 159087012594 dimerization interface [polypeptide binding]; other site 159087012595 putative substrate binding pocket [chemical binding]; other site 159087012596 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 159087012597 PAS domain S-box; Region: sensory_box; TIGR00229 159087012598 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 159087012599 putative active site [active] 159087012600 heme pocket [chemical binding]; other site 159087012601 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 159087012602 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 159087012603 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 159087012604 tetramer interface [polypeptide binding]; other site 159087012605 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 159087012606 tetramer interface [polypeptide binding]; other site 159087012607 active site 159087012608 Fe binding site [ion binding]; other site 159087012609 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 159087012610 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 159087012611 NAD binding site [chemical binding]; other site 159087012612 catalytic residues [active] 159087012613 acetaldehyde dehydrogenase; Validated; Region: PRK08300 159087012614 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 159087012615 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 159087012616 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 159087012617 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 159087012618 active site 159087012619 catalytic residues [active] 159087012620 metal binding site [ion binding]; metal-binding site 159087012621 DmpG-like communication domain; Region: DmpG_comm; pfam07836 159087012622 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087012623 active site 159087012624 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 159087012625 active site 1 [active] 159087012626 dimer interface [polypeptide binding]; other site 159087012627 hexamer interface [polypeptide binding]; other site 159087012628 active site 2 [active] 159087012629 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 159087012630 active site 1 [active] 159087012631 dimer interface [polypeptide binding]; other site 159087012632 hexamer interface [polypeptide binding]; other site 159087012633 active site 2 [active] 159087012634 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 159087012635 dimerization interface [polypeptide binding]; other site 159087012636 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087012637 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087012638 dimer interface [polypeptide binding]; other site 159087012639 putative CheW interface [polypeptide binding]; other site 159087012640 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 159087012641 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 159087012642 active site 159087012643 phosphorylation site [posttranslational modification] 159087012644 intermolecular recognition site; other site 159087012645 dimerization interface [polypeptide binding]; other site 159087012646 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 159087012647 DNA binding residues [nucleotide binding] 159087012648 dimerization interface [polypeptide binding]; other site 159087012649 PAS domain S-box; Region: sensory_box; TIGR00229 159087012650 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 159087012651 putative active site [active] 159087012652 heme pocket [chemical binding]; other site 159087012653 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 159087012654 dimer interface [polypeptide binding]; other site 159087012655 phosphorylation site [posttranslational modification] 159087012656 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 159087012657 ATP binding site [chemical binding]; other site 159087012658 Mg2+ binding site [ion binding]; other site 159087012659 G-X-G motif; other site 159087012660 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012661 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 159087012662 active site 159087012663 phosphorylation site [posttranslational modification] 159087012664 intermolecular recognition site; other site 159087012665 dimerization interface [polypeptide binding]; other site 159087012666 PAS domain S-box; Region: sensory_box; TIGR00229 159087012667 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 159087012668 putative active site [active] 159087012669 heme pocket [chemical binding]; other site 159087012670 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 159087012671 dimer interface [polypeptide binding]; other site 159087012672 phosphorylation site [posttranslational modification] 159087012673 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 159087012674 ATP binding site [chemical binding]; other site 159087012675 G-X-G motif; other site 159087012676 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 159087012677 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 159087012678 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 159087012679 catalytic loop [active] 159087012680 iron binding site [ion binding]; other site 159087012681 Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P; Region: T4MO_e_transfer_like; cd06190 159087012682 FAD binding pocket [chemical binding]; other site 159087012683 FAD binding motif [chemical binding]; other site 159087012684 phosphate binding motif [ion binding]; other site 159087012685 beta-alpha-beta structure motif; other site 159087012686 NAD binding pocket [chemical binding]; other site 159087012687 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 159087012688 dimerization interface [polypeptide binding]; other site 159087012689 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 159087012690 Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent...; Region: Rieske_T4moC; cd03474 159087012691 [2Fe-2S] cluster binding site [ion binding]; other site 159087012692 Toluene-4-monooxygenase system protein B (TmoB); Region: TmoB; pfam06234 159087012693 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 159087012694 dinuclear metal binding motif [ion binding]; other site 159087012695 Cache domain; Region: Cache_1; pfam02743 159087012696 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087012697 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 159087012698 dimerization interface [polypeptide binding]; other site 159087012699 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 159087012700 dimer interface [polypeptide binding]; other site 159087012701 phosphorylation site [posttranslational modification] 159087012702 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 159087012703 ATP binding site [chemical binding]; other site 159087012704 Mg2+ binding site [ion binding]; other site 159087012705 G-X-G motif; other site 159087012706 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012707 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 159087012708 active site 159087012709 phosphorylation site [posttranslational modification] 159087012710 intermolecular recognition site; other site 159087012711 dimerization interface [polypeptide binding]; other site 159087012712 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 159087012713 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 159087012714 putative active site [active] 159087012715 putative NTP binding site [chemical binding]; other site 159087012716 putative nucleic acid binding site [nucleotide binding]; other site 159087012717 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 159087012718 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 159087012719 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 159087012720 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 159087012721 phosphodiesterase YaeI; Provisional; Region: PRK11340 159087012722 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 159087012723 putative active site [active] 159087012724 putative metal binding site [ion binding]; other site 159087012725 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 159087012726 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 159087012727 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087012728 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 159087012729 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087012730 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 159087012731 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 159087012732 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087012733 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087012734 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 159087012735 putative effector binding pocket; other site 159087012736 putative dimerization interface [polypeptide binding]; other site 159087012737 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 159087012738 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 159087012739 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR6; cd08272 159087012740 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 159087012741 putative NAD(P) binding site [chemical binding]; other site 159087012742 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087012743 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087012744 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 159087012745 dimerization interface [polypeptide binding]; other site 159087012746 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 159087012747 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 159087012748 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 159087012749 dimer interface [polypeptide binding]; other site 159087012750 active site 159087012751 heme binding site [chemical binding]; other site 159087012752 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 159087012753 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 159087012754 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 159087012755 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 159087012756 DNA binding residues [nucleotide binding] 159087012757 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 159087012758 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087012759 4Fe-4S binding domain; Region: Fer4_5; pfam12801 159087012760 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 159087012761 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 159087012762 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 159087012763 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 159087012764 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 159087012765 active site 159087012766 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 159087012767 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 159087012768 HD domain; Region: HD_4; pfam13328 159087012769 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 159087012770 synthetase active site [active] 159087012771 NTP binding site [chemical binding]; other site 159087012772 metal binding site [ion binding]; metal-binding site 159087012773 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 159087012774 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 159087012775 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 159087012776 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 159087012777 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 159087012778 catalytic site [active] 159087012779 G-X2-G-X-G-K; other site 159087012780 PAS domain S-box; Region: sensory_box; TIGR00229 159087012781 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 159087012782 putative active site [active] 159087012783 heme pocket [chemical binding]; other site 159087012784 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 159087012785 dimer interface [polypeptide binding]; other site 159087012786 phosphorylation site [posttranslational modification] 159087012787 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 159087012788 ATP binding site [chemical binding]; other site 159087012789 Mg2+ binding site [ion binding]; other site 159087012790 G-X-G motif; other site 159087012791 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012792 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 159087012793 active site 159087012794 phosphorylation site [posttranslational modification] 159087012795 intermolecular recognition site; other site 159087012796 dimerization interface [polypeptide binding]; other site 159087012797 hypothetical protein; Provisional; Region: PRK11820 159087012798 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 159087012799 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 159087012800 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 159087012801 Catalytic domain of Protein Kinases; Region: PKc; cd00180 159087012802 active site 159087012803 ATP binding site [chemical binding]; other site 159087012804 substrate binding site [chemical binding]; other site 159087012805 activation loop (A-loop); other site 159087012806 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 159087012807 active site 159087012808 ribonuclease PH; Reviewed; Region: rph; PRK00173 159087012809 Ribonuclease PH; Region: RNase_PH_bact; cd11362 159087012810 hexamer interface [polypeptide binding]; other site 159087012811 active site 159087012812 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 159087012813 active site 159087012814 dimerization interface [polypeptide binding]; other site 159087012815 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 159087012816 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 159087012817 FeS/SAM binding site; other site 159087012818 HemN C-terminal domain; Region: HemN_C; pfam06969 159087012819 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087012820 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087012821 ligand binding site [chemical binding]; other site 159087012822 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 159087012823 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 159087012824 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087012825 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087012826 ABC transporter; Region: ABC_tran_2; pfam12848 159087012827 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 159087012828 SEC-C motif; Region: SEC-C; pfam02810 159087012829 hypothetical protein; Provisional; Region: PRK01842 159087012830 recombination associated protein; Reviewed; Region: rdgC; PRK00321 159087012831 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 159087012832 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 159087012833 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 159087012834 S-adenosylmethionine binding site [chemical binding]; other site 159087012835 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 159087012836 ThiS interaction site; other site 159087012837 putative active site [active] 159087012838 tetramer interface [polypeptide binding]; other site 159087012839 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 159087012840 thiS-thiF/thiG interaction site; other site 159087012841 short chain dehydrogenase; Provisional; Region: PRK07024 159087012842 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087012843 NAD(P) binding site [chemical binding]; other site 159087012844 active site 159087012845 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 159087012846 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 159087012847 catalytic residues [active] 159087012848 hinge region; other site 159087012849 alpha helical domain; other site 159087012850 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 159087012851 Sporulation related domain; Region: SPOR; pfam05036 159087012852 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 159087012853 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 159087012854 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 159087012855 active site 159087012856 HIGH motif; other site 159087012857 nucleotide binding site [chemical binding]; other site 159087012858 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 159087012859 KMSK motif region; other site 159087012860 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 159087012861 tRNA binding surface [nucleotide binding]; other site 159087012862 anticodon binding site; other site 159087012863 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 159087012864 putative active site [active] 159087012865 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087012866 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087012867 metal binding site [ion binding]; metal-binding site 159087012868 active site 159087012869 I-site; other site 159087012870 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 159087012871 ABC1 family; Region: ABC1; pfam03109 159087012872 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; cd05120 159087012873 active site 159087012874 ATP binding site [chemical binding]; other site 159087012875 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 159087012876 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 159087012877 ATP binding site [chemical binding]; other site 159087012878 putative Mg++ binding site [ion binding]; other site 159087012879 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 159087012880 nucleotide binding region [chemical binding]; other site 159087012881 ATP-binding site [chemical binding]; other site 159087012882 Domain of unknown function DUF302; Region: DUF302; cl01364 159087012883 PAS fold; Region: PAS_4; pfam08448 159087012884 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 159087012885 putative active site [active] 159087012886 heme pocket [chemical binding]; other site 159087012887 PAS domain; Region: PAS_9; pfam13426 159087012888 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 159087012889 putative active site [active] 159087012890 heme pocket [chemical binding]; other site 159087012891 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087012892 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 159087012893 dimer interface [polypeptide binding]; other site 159087012894 phosphorylation site [posttranslational modification] 159087012895 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 159087012896 ATP binding site [chemical binding]; other site 159087012897 Mg2+ binding site [ion binding]; other site 159087012898 G-X-G motif; other site 159087012899 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012900 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 159087012901 active site 159087012902 phosphorylation site [posttranslational modification] 159087012903 intermolecular recognition site; other site 159087012904 dimerization interface [polypeptide binding]; other site 159087012905 Uncharacterized conserved protein [Function unknown]; Region: COG3287 159087012906 FIST N domain; Region: FIST; pfam08495 159087012907 FIST C domain; Region: FIST_C; pfam10442 159087012908 Competence-damaged protein; Region: CinA; cl00666 159087012909 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 159087012910 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 159087012911 GTP binding site; other site 159087012912 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 159087012913 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 159087012914 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 159087012915 Part of AAA domain; Region: AAA_19; pfam13245 159087012916 Family description; Region: UvrD_C_2; pfam13538 159087012917 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 159087012918 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 159087012919 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 159087012920 Walker A motif; other site 159087012921 ATP binding site [chemical binding]; other site 159087012922 Walker B motif; other site 159087012923 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 159087012924 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 159087012925 Walker A motif; other site 159087012926 ATP binding site [chemical binding]; other site 159087012927 Walker B motif; other site 159087012928 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 159087012929 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 159087012930 catalytic residue [active] 159087012931 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 159087012932 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 159087012933 YGGT family; Region: YGGT; pfam02325 159087012934 Uncharacterized ACR, YggU family COG1872; Region: DUF167; pfam02594 159087012935 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 159087012936 Helix-hairpin-helix motif; Region: HHH; pfam00633 159087012937 dihydroorotase; Provisional; Region: PRK07627 159087012938 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 159087012939 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 159087012940 active site 159087012941 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 159087012942 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 159087012943 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 159087012944 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 159087012945 active site 159087012946 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 159087012947 hypothetical protein; Validated; Region: PRK00228 159087012948 DNA photolyase; Region: DNA_photolyase; pfam00875 159087012949 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 159087012950 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 159087012951 putative binding surface; other site 159087012952 active site 159087012953 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 159087012954 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 159087012955 putative binding surface; other site 159087012956 active site 159087012957 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 159087012958 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 159087012959 ATP binding site [chemical binding]; other site 159087012960 Mg2+ binding site [ion binding]; other site 159087012961 G-X-G motif; other site 159087012962 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087012963 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012964 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 159087012965 active site 159087012966 phosphorylation site [posttranslational modification] 159087012967 intermolecular recognition site; other site 159087012968 dimerization interface [polypeptide binding]; other site 159087012969 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 159087012970 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 159087012971 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 159087012972 dimer interface [polypeptide binding]; other site 159087012973 putative CheW interface [polypeptide binding]; other site 159087012974 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 159087012975 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012976 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 159087012977 active site 159087012978 phosphorylation site [posttranslational modification] 159087012979 intermolecular recognition site; other site 159087012980 dimerization interface [polypeptide binding]; other site 159087012981 Response regulator receiver domain; Region: Response_reg; pfam00072 159087012982 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 159087012983 active site 159087012984 phosphorylation site [posttranslational modification] 159087012985 intermolecular recognition site; other site 159087012986 dimerization interface [polypeptide binding]; other site 159087012987 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 159087012988 substrate binding site [chemical binding]; other site 159087012989 dimer interface [polypeptide binding]; other site 159087012990 ATP binding site [chemical binding]; other site 159087012991 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 159087012992 thiamine phosphate binding site [chemical binding]; other site 159087012993 active site 159087012994 pyrophosphate binding site [ion binding]; other site 159087012995 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 159087012996 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 159087012997 inhibitor-cofactor binding pocket; inhibition site 159087012998 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087012999 catalytic residue [active] 159087013000 multidrug efflux system protein; Provisional; Region: PRK11431 159087013001 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 159087013002 Sulfate transporter family; Region: Sulfate_transp; pfam00916 159087013003 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 159087013004 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087013005 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 159087013006 ligand binding site [chemical binding]; other site 159087013007 flexible hinge region; other site 159087013008 MgtE intracellular N domain; Region: MgtE_N; smart00924 159087013009 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 159087013010 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 159087013011 Cl binding site [ion binding]; other site 159087013012 oligomer interface [polypeptide binding]; other site 159087013013 Transglycosylase; Region: Transgly; cl17702 159087013014 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 159087013015 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 159087013016 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 159087013017 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 159087013018 shikimate binding site; other site 159087013019 NAD(P) binding site [chemical binding]; other site 159087013020 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 159087013021 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 159087013022 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 159087013023 RNB domain; Region: RNB; pfam00773 159087013024 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 159087013025 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087013026 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 159087013027 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087013028 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087013029 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087013030 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 159087013031 dimerization interface [polypeptide binding]; other site 159087013032 substrate binding pocket [chemical binding]; other site 159087013033 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 159087013034 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 159087013035 FtsX-like permease family; Region: FtsX; pfam02687 159087013036 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 159087013037 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 159087013038 Walker A/P-loop; other site 159087013039 ATP binding site [chemical binding]; other site 159087013040 Q-loop/lid; other site 159087013041 ABC transporter signature motif; other site 159087013042 Walker B; other site 159087013043 D-loop; other site 159087013044 H-loop/switch region; other site 159087013045 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 159087013046 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 159087013047 HlyD family secretion protein; Region: HlyD_3; pfam13437 159087013048 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 159087013049 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 159087013050 dimer interface [polypeptide binding]; other site 159087013051 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 159087013052 ThiC-associated domain; Region: ThiC-associated; pfam13667 159087013053 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 159087013054 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 159087013055 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 159087013056 active site 159087013057 zinc binding site [ion binding]; other site 159087013058 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 159087013059 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 159087013060 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 159087013061 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 159087013062 S-adenosylmethionine binding site [chemical binding]; other site 159087013063 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains; Region: RHOD_2; cd01528 159087013064 active site residue [active] 159087013065 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 159087013066 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 159087013067 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 159087013068 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 159087013069 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 159087013070 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 159087013071 putative active site [active] 159087013072 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 159087013073 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 159087013074 putative metal binding site; other site 159087013075 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 159087013076 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 159087013077 putative NAD(P) binding site [chemical binding]; other site 159087013078 active site 159087013079 putative substrate binding site [chemical binding]; other site 159087013080 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 159087013081 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 159087013082 glutaminase active site [active] 159087013083 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 159087013084 dimer interface [polypeptide binding]; other site 159087013085 active site 159087013086 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 159087013087 dimer interface [polypeptide binding]; other site 159087013088 active site 159087013089 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 159087013090 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 159087013091 active site 159087013092 metal binding site [ion binding]; metal-binding site 159087013093 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087013094 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 159087013095 putative acyl-acceptor binding pocket; other site 159087013096 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 159087013097 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 159087013098 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 159087013099 substrate binding site [chemical binding]; other site 159087013100 ATP binding site [chemical binding]; other site 159087013101 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 159087013102 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 159087013103 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 159087013104 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 159087013105 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087013106 ATP-grasp domain; Region: ATP-grasp_4; cl17255 159087013107 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 159087013108 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 159087013109 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 159087013110 carboxyltransferase (CT) interaction site; other site 159087013111 biotinylation site [posttranslational modification]; other site 159087013112 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 159087013113 Dehydroquinase class II; Region: DHquinase_II; pfam01220 159087013114 trimer interface [polypeptide binding]; other site 159087013115 active site 159087013116 dimer interface [polypeptide binding]; other site 159087013117 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 159087013118 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 159087013119 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 159087013120 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 159087013121 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 159087013122 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 159087013123 Malic enzyme, N-terminal domain; Region: malic; pfam00390 159087013124 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 159087013125 putative NAD(P) binding site [chemical binding]; other site 159087013126 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 159087013127 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087013128 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 159087013129 N-terminal plug; other site 159087013130 ligand-binding site [chemical binding]; other site 159087013131 High-affinity nickel-transport protein; Region: NicO; cl00964 159087013132 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 159087013133 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 159087013134 putative active site [active] 159087013135 heme pocket [chemical binding]; other site 159087013136 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 159087013137 dimer interface [polypeptide binding]; other site 159087013138 phosphorylation site [posttranslational modification] 159087013139 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 159087013140 ATP binding site [chemical binding]; other site 159087013141 G-X-G motif; other site 159087013142 nickel responsive regulator; Provisional; Region: PRK02967 159087013143 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 159087013144 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 159087013145 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 159087013146 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 159087013147 Walker A motif; other site 159087013148 ATP binding site [chemical binding]; other site 159087013149 Walker B motif; other site 159087013150 arginine finger; other site 159087013151 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 159087013152 HSP70 interaction site [polypeptide binding]; other site 159087013153 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 159087013154 PAS domain; Region: PAS_9; pfam13426 159087013155 putative active site [active] 159087013156 heme pocket [chemical binding]; other site 159087013157 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087013158 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087013159 metal binding site [ion binding]; metal-binding site 159087013160 active site 159087013161 I-site; other site 159087013162 Hemerythrin; Region: Hemerythrin; cd12107 159087013163 Fe binding site [ion binding]; other site 159087013164 Fic family protein [Function unknown]; Region: COG3177 159087013165 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 159087013166 Fic/DOC family; Region: Fic; pfam02661 159087013167 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 159087013168 Helix-turn-helix domain; Region: HTH_38; pfam13936 159087013169 Homeodomain-like domain; Region: HTH_32; pfam13565 159087013170 Integrase core domain; Region: rve; pfam00665 159087013171 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 159087013172 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 159087013173 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 159087013174 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 159087013175 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 159087013176 active site 159087013177 phosphorylation site [posttranslational modification] 159087013178 intermolecular recognition site; other site 159087013179 dimerization interface [polypeptide binding]; other site 159087013180 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 159087013181 Walker A motif; other site 159087013182 ATP binding site [chemical binding]; other site 159087013183 Walker B motif; other site 159087013184 arginine finger; other site 159087013185 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 159087013186 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 159087013187 HypX protein, N-terminal hydrolase domain; Region: FMT_core_HypX_N; cd08650 159087013188 putative active site [active] 159087013189 putative substrate binding site [chemical binding]; other site 159087013190 putative cosubstrate binding site; other site 159087013191 catalytic site [active] 159087013192 C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins; Region: FMT_C_HypX; cd08701 159087013193 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 159087013194 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 159087013195 substrate binding site [chemical binding]; other site 159087013196 oxyanion hole (OAH) forming residues; other site 159087013197 trimer interface [polypeptide binding]; other site 159087013198 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 159087013199 dimerization interface [polypeptide binding]; other site 159087013200 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 159087013201 ATP binding site [chemical binding]; other site 159087013202 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 159087013203 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 159087013204 HupF/HypC family; Region: HupF_HypC; pfam01455 159087013205 [NiFe] hydrogenase assembly chaperone, HybE family; Region: hydrog_HybE; TIGR03993 159087013206 HupF/HypC family; Region: HupF_HypC; pfam01455 159087013207 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 159087013208 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 159087013209 putative substrate-binding site; other site 159087013210 nickel binding site [ion binding]; other site 159087013211 hydrogenase 2 large subunit; Provisional; Region: PRK10467 159087013212 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 159087013213 putative hydrogenase 2 b cytochrome subunit; Provisional; Region: PRK10881 159087013214 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 159087013215 hydrogenase 2 protein HybA; Provisional; Region: PRK10882 159087013216 4Fe-4S binding domain; Region: Fer4_6; pfam12837 159087013217 hydrogenase 2 small subunit; Provisional; Region: PRK10468 159087013218 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 159087013219 CHASE domain; Region: CHASE; pfam03924 159087013220 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087013221 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087013222 metal binding site [ion binding]; metal-binding site 159087013223 active site 159087013224 I-site; other site 159087013225 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 159087013226 substrate binding pocket [chemical binding]; other site 159087013227 membrane-bound complex binding site; other site 159087013228 hinge residues; other site 159087013229 Acylphosphatase; Region: Acylphosphatase; pfam00708 159087013230 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 159087013231 HypF finger; Region: zf-HYPF; pfam07503 159087013232 HypF finger; Region: zf-HYPF; pfam07503 159087013233 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 159087013234 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 159087013235 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 159087013236 Hydrogenase expression/synthesis hypA family; Region: HypA; cl17671 159087013237 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 159087013238 [NiFe] hydrogenase assembly chaperone, HybE family; Region: hydrog_HybE; TIGR03993 159087013239 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 159087013240 Rubredoxin; Region: Rubredoxin; pfam00301 159087013241 iron binding site [ion binding]; other site 159087013242 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 159087013243 HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the...; Region: HyaE; cd02965 159087013244 HupF/HypC family; Region: HupF_HypC; pfam01455 159087013245 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 159087013246 putative substrate-binding site; other site 159087013247 nickel binding site [ion binding]; other site 159087013248 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 159087013249 hydrogenase 1 large subunit; Provisional; Region: PRK10170 159087013250 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 159087013251 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 159087013252 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 159087013253 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 159087013254 FOG: CBS domain [General function prediction only]; Region: COG0517 159087013255 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 159087013256 FOG: CBS domain [General function prediction only]; Region: COG0517 159087013257 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 159087013258 FOG: CBS domain [General function prediction only]; Region: COG0517 159087013259 PAS fold; Region: PAS_4; pfam08448 159087013260 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 159087013261 GAF domain; Region: GAF; pfam01590 159087013262 PAS domain S-box; Region: sensory_box; TIGR00229 159087013263 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 159087013264 putative active site [active] 159087013265 heme pocket [chemical binding]; other site 159087013266 PAS domain S-box; Region: sensory_box; TIGR00229 159087013267 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 159087013268 putative active site [active] 159087013269 heme pocket [chemical binding]; other site 159087013270 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 159087013271 PAS domain; Region: PAS_9; pfam13426 159087013272 putative active site [active] 159087013273 heme pocket [chemical binding]; other site 159087013274 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087013275 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087013276 metal binding site [ion binding]; metal-binding site 159087013277 active site 159087013278 I-site; other site 159087013279 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 159087013280 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 159087013281 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 159087013282 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 159087013283 Walker A/P-loop; other site 159087013284 ATP binding site [chemical binding]; other site 159087013285 Q-loop/lid; other site 159087013286 ABC transporter signature motif; other site 159087013287 Walker B; other site 159087013288 D-loop; other site 159087013289 H-loop/switch region; other site 159087013290 CcmB protein; Region: CcmB; pfam03379 159087013291 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 159087013292 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 159087013293 CcmE; Region: CcmE; pfam03100 159087013294 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 159087013295 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 159087013296 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 159087013297 catalytic residues [active] 159087013298 central insert; other site 159087013299 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 159087013300 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 159087013301 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 159087013302 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 159087013303 binding surface 159087013304 TPR motif; other site 159087013305 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087013306 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 159087013307 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 159087013308 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 159087013309 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 159087013310 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 159087013311 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 159087013312 carboxyltransferase (CT) interaction site; other site 159087013313 biotinylation site [posttranslational modification]; other site 159087013314 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 159087013315 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 159087013316 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 159087013317 membrane ATPase/protein kinase; Provisional; Region: PRK09435 159087013318 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 159087013319 Walker A; other site 159087013320 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 159087013321 G4 box; other site 159087013322 G5 box; other site 159087013323 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 159087013324 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 159087013325 active site 159087013326 substrate binding site [chemical binding]; other site 159087013327 coenzyme B12 binding site [chemical binding]; other site 159087013328 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 159087013329 B12 binding site [chemical binding]; other site 159087013330 cobalt ligand [ion binding]; other site 159087013331 Transcriptional regulators [Transcription]; Region: GntR; COG1802 159087013332 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087013333 DNA-binding site [nucleotide binding]; DNA binding site 159087013334 FCD domain; Region: FCD; pfam07729 159087013335 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 159087013336 PAS fold; Region: PAS_3; pfam08447 159087013337 putative active site [active] 159087013338 heme pocket [chemical binding]; other site 159087013339 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 159087013340 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 159087013341 Na binding site [ion binding]; other site 159087013342 Protein of unknown function, DUF485; Region: DUF485; pfam04341 159087013343 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 159087013344 enoyl-CoA hydratase; Provisional; Region: PRK06127 159087013345 substrate binding site [chemical binding]; other site 159087013346 oxyanion hole (OAH) forming residues; other site 159087013347 trimer interface [polypeptide binding]; other site 159087013348 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087013349 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 159087013350 malonate decarboxylase, epsilon subunit; Region: malonate_mdcH; TIGR03131 159087013351 triphosphoribosyl-dephospho-CoA synthase MdcB; Region: malonate_mdcB; TIGR03132 159087013352 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; pfam10620 159087013353 malonate decarboxylase holo-[acyl-carrier-protein] synthase; Region: malonate_mdcG; TIGR03135 159087013354 malonate decarboxylase, gamma subunit; Region: malonate_gamma; TIGR03134 159087013355 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189 159087013356 malonate decarboxylase acyl carrier protein; Region: malonate_delta; TIGR03130 159087013357 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 159087013358 DctM-like transporters; Region: DctM; pfam06808 159087013359 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 159087013360 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 159087013361 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 159087013362 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 159087013363 Transcriptional regulators [Transcription]; Region: GntR; COG1802 159087013364 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 159087013365 DNA-binding site [nucleotide binding]; DNA binding site 159087013366 FCD domain; Region: FCD; pfam07729 159087013367 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 159087013368 EVE domain; Region: EVE; cl00728 159087013369 Cell division protein ZapA; Region: ZapA; pfam05164 159087013370 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087013371 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 159087013372 N-terminal plug; other site 159087013373 ligand-binding site [chemical binding]; other site 159087013374 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 159087013375 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 159087013376 N-terminal plug; other site 159087013377 ligand-binding site [chemical binding]; other site 159087013378 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 159087013379 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 159087013380 ABC-ATPase subunit interface; other site 159087013381 dimer interface [polypeptide binding]; other site 159087013382 putative PBP binding regions; other site 159087013383 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 159087013384 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 159087013385 Walker A/P-loop; other site 159087013386 ATP binding site [chemical binding]; other site 159087013387 Q-loop/lid; other site 159087013388 ABC transporter signature motif; other site 159087013389 Walker B; other site 159087013390 D-loop; other site 159087013391 H-loop/switch region; other site 159087013392 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 159087013393 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated; Region: PRK05986 159087013394 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 159087013395 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 159087013396 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 159087013397 catalytic triad [active] 159087013398 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 159087013399 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087013400 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 159087013401 dimerization interface [polypeptide binding]; other site 159087013402 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 159087013403 dimer interface [polypeptide binding]; other site 159087013404 phosphorylation site [posttranslational modification] 159087013405 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 159087013406 ATP binding site [chemical binding]; other site 159087013407 Mg2+ binding site [ion binding]; other site 159087013408 G-X-G motif; other site 159087013409 Response regulator receiver domain; Region: Response_reg; pfam00072 159087013410 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 159087013411 active site 159087013412 phosphorylation site [posttranslational modification] 159087013413 intermolecular recognition site; other site 159087013414 dimerization interface [polypeptide binding]; other site 159087013415 hypothetical protein; Validated; Region: PRK00029 159087013416 Uncharacterized conserved protein [Function unknown]; Region: COG0397 159087013417 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 159087013418 Predicted transporter component [General function prediction only]; Region: COG2391 159087013419 Sulphur transport; Region: Sulf_transp; pfam04143 159087013420 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 159087013421 Ligand Binding Site [chemical binding]; other site 159087013422 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 159087013423 Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; Region: PBP1_Nba_like; cd06359 159087013424 putative ligand binding site [chemical binding]; other site 159087013425 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087013426 TM-ABC transporter signature motif; other site 159087013427 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087013428 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087013429 TM-ABC transporter signature motif; other site 159087013430 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087013431 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087013432 Walker A/P-loop; other site 159087013433 ATP binding site [chemical binding]; other site 159087013434 Q-loop/lid; other site 159087013435 ABC transporter signature motif; other site 159087013436 Walker B; other site 159087013437 D-loop; other site 159087013438 H-loop/switch region; other site 159087013439 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087013440 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087013441 Walker A/P-loop; other site 159087013442 ATP binding site [chemical binding]; other site 159087013443 Q-loop/lid; other site 159087013444 ABC transporter signature motif; other site 159087013445 Walker B; other site 159087013446 D-loop; other site 159087013447 H-loop/switch region; other site 159087013448 PAS domain S-box; Region: sensory_box; TIGR00229 159087013449 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 159087013450 putative active site [active] 159087013451 heme pocket [chemical binding]; other site 159087013452 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 159087013453 PAS domain; Region: PAS_9; pfam13426 159087013454 putative active site [active] 159087013455 heme pocket [chemical binding]; other site 159087013456 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 159087013457 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 159087013458 metal binding site [ion binding]; metal-binding site 159087013459 active site 159087013460 I-site; other site 159087013461 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 159087013462 PilZ domain; Region: PilZ; pfam07238 159087013463 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 159087013464 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 159087013465 FeS/SAM binding site; other site 159087013466 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 159087013467 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 159087013468 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 159087013469 ligand binding site [chemical binding]; other site 159087013470 translocation protein TolB; Provisional; Region: tolB; PRK02889 159087013471 TolB amino-terminal domain; Region: TolB_N; pfam04052 159087013472 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 159087013473 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 159087013474 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 159087013475 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 159087013476 TonB C terminal; Region: TonB_2; pfam13103 159087013477 TolA protein; Region: tolA_full; TIGR02794 159087013478 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 159087013479 TolR protein; Region: tolR; TIGR02801 159087013480 TolQ protein; Region: tolQ; TIGR02796 159087013481 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 159087013482 active site 159087013483 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 159087013484 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4402 159087013485 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 159087013486 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 159087013487 Walker A motif; other site 159087013488 ATP binding site [chemical binding]; other site 159087013489 Walker B motif; other site 159087013490 arginine finger; other site 159087013491 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 159087013492 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 159087013493 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 159087013494 RuvA N terminal domain; Region: RuvA_N; pfam01330 159087013495 Pathogenicity locus; Region: Cdd1; pfam11731 159087013496 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 159087013497 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 159087013498 active site 159087013499 putative DNA-binding cleft [nucleotide binding]; other site 159087013500 dimer interface [polypeptide binding]; other site 159087013501 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 159087013502 EamA-like transporter family; Region: EamA; pfam00892 159087013503 hypothetical protein; Validated; Region: PRK00110 159087013504 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 159087013505 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 159087013506 PBP superfamily domain; Region: PBP_like_2; cl17296 159087013507 N-acetylmuramoyl-L-alanine amidase; Region: Amidase_2; pfam01510 159087013508 Bacterial SH3 domain; Region: SH3_3; pfam08239 159087013509 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 159087013510 putative hydrophobic ligand binding site [chemical binding]; other site 159087013511 Uncharacterized conserved protein [Function unknown]; Region: COG3791 159087013512 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 159087013513 EamA-like transporter family; Region: EamA; pfam00892 159087013514 EamA-like transporter family; Region: EamA; pfam00892 159087013515 Chorismate mutase type II; Region: CM_2; smart00830 159087013516 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 159087013517 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087013518 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 159087013519 dimerization interface [polypeptide binding]; other site 159087013520 substrate binding pocket [chemical binding]; other site 159087013521 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 159087013522 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 159087013523 homodimer interface [polypeptide binding]; other site 159087013524 substrate-cofactor binding pocket; other site 159087013525 catalytic residue [active] 159087013526 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 159087013527 Transcriptional regulator [Transcription]; Region: LysR; COG0583 159087013528 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 159087013529 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 159087013530 putative dimerization interface [polypeptide binding]; other site 159087013531 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 159087013532 EamA-like transporter family; Region: EamA; pfam00892 159087013533 EamA-like transporter family; Region: EamA; pfam00892 159087013534 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cl00025 159087013535 active pocket/dimerization site; other site 159087013536 active site 159087013537 phosphorylation site [posttranslational modification] 159087013538 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 159087013539 dimerization domain swap beta strand [polypeptide binding]; other site 159087013540 regulatory protein interface [polypeptide binding]; other site 159087013541 active site 159087013542 regulatory phosphorylation site [posttranslational modification]; other site 159087013543 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 159087013544 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 159087013545 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 159087013546 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 159087013547 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 159087013548 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 159087013549 membrane-bound complex binding site; other site 159087013550 hinge residues; other site 159087013551 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 159087013552 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 159087013553 dimerization interface [polypeptide binding]; other site 159087013554 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 159087013555 dimer interface [polypeptide binding]; other site 159087013556 phosphorylation site [posttranslational modification] 159087013557 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 159087013558 ATP binding site [chemical binding]; other site 159087013559 Mg2+ binding site [ion binding]; other site 159087013560 G-X-G motif; other site 159087013561 Response regulator receiver domain; Region: Response_reg; pfam00072 159087013562 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 159087013563 active site 159087013564 phosphorylation site [posttranslational modification] 159087013565 intermolecular recognition site; other site 159087013566 dimerization interface [polypeptide binding]; other site 159087013567 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 159087013568 Sel1-like repeats; Region: SEL1; smart00671 159087013569 Sel1-like repeats; Region: SEL1; smart00671 159087013570 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 159087013571 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 159087013572 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 159087013573 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 159087013574 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 159087013575 putative switch regulator; other site 159087013576 non-specific DNA interactions [nucleotide binding]; other site 159087013577 DNA binding site [nucleotide binding] 159087013578 sequence specific DNA binding site [nucleotide binding]; other site 159087013579 putative cAMP binding site [chemical binding]; other site 159087013580 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 159087013581 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 159087013582 N-terminal plug; other site 159087013583 ligand-binding site [chemical binding]; other site 159087013584 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 159087013585 catalytic residues [active] 159087013586 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 159087013587 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 159087013588 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 159087013589 Lumazine binding domain; Region: Lum_binding; pfam00677 159087013590 Lumazine binding domain; Region: Lum_binding; pfam00677 159087013591 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087013592 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087013593 putative ligand binding site [chemical binding]; other site 159087013594 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087013595 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 159087013596 putative ligand binding site [chemical binding]; other site 159087013597 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 159087013598 TM-ABC transporter signature motif; other site 159087013599 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 159087013600 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 159087013601 TM-ABC transporter signature motif; other site 159087013602 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 159087013603 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 159087013604 Walker A/P-loop; other site 159087013605 ATP binding site [chemical binding]; other site 159087013606 Q-loop/lid; other site 159087013607 ABC transporter signature motif; other site 159087013608 Walker B; other site 159087013609 D-loop; other site 159087013610 H-loop/switch region; other site 159087013611 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 159087013612 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 159087013613 Walker A/P-loop; other site 159087013614 ATP binding site [chemical binding]; other site 159087013615 Q-loop/lid; other site 159087013616 ABC transporter signature motif; other site 159087013617 Walker B; other site 159087013618 D-loop; other site 159087013619 H-loop/switch region; other site 159087013620 membrane protein P6; Region: PHA01399 159087013621 Response regulator receiver domain; Region: Response_reg; pfam00072 159087013622 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 159087013623 active site 159087013624 phosphorylation site [posttranslational modification] 159087013625 intermolecular recognition site; other site 159087013626 dimerization interface [polypeptide binding]; other site 159087013627 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 159087013628 binding surface 159087013629 TPR motif; other site 159087013630 Tetratricopeptide repeat; Region: TPR_16; pfam13432 159087013631 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 159087013632 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 159087013633 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 159087013634 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 159087013635 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 159087013636 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 159087013637 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 159087013638 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 159087013639 P-loop; other site 159087013640 Magnesium ion binding site [ion binding]; other site 159087013641 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 159087013642 Magnesium ion binding site [ion binding]; other site 159087013643 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 159087013644 ParB-like nuclease domain; Region: ParB; smart00470 159087013645 ATP synthase I chain; Region: ATP_synt_I; cl09170 159087013646 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 159087013647 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 159087013648 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 159087013649 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 159087013650 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 159087013651 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 159087013652 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 159087013653 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 159087013654 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 159087013655 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 159087013656 beta subunit interaction interface [polypeptide binding]; other site 159087013657 Walker A motif; other site 159087013658 ATP binding site [chemical binding]; other site 159087013659 Walker B motif; other site 159087013660 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 159087013661 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 159087013662 core domain interface [polypeptide binding]; other site 159087013663 delta subunit interface [polypeptide binding]; other site 159087013664 epsilon subunit interface [polypeptide binding]; other site 159087013665 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 159087013666 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 159087013667 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 159087013668 alpha subunit interaction interface [polypeptide binding]; other site 159087013669 Walker A motif; other site 159087013670 ATP binding site [chemical binding]; other site 159087013671 Walker B motif; other site 159087013672 inhibitor binding site; inhibition site 159087013673 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 159087013674 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 159087013675 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 159087013676 gamma subunit interface [polypeptide binding]; other site 159087013677 epsilon subunit interface [polypeptide binding]; other site 159087013678 LBP interface [polypeptide binding]; other site 159087013679 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 159087013680 SCP-2 sterol transfer family; Region: SCP2; pfam02036 159087013681 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 159087013682 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 159087013683 S-adenosylmethionine binding site [chemical binding]; other site 159087013684 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 159087013685 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 159087013686 nucleotide binding site/active site [active] 159087013687 HIT family signature motif; other site 159087013688 catalytic residue [active] 159087013689 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 159087013690 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087013691 FAD binding domain; Region: FAD_binding_4; pfam01565 159087013692 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 159087013693 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 159087013694 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 159087013695 Cysteine-rich domain; Region: CCG; pfam02754 159087013696 Cysteine-rich domain; Region: CCG; pfam02754 159087013697 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 159087013698 Predicted membrane protein [Function unknown]; Region: COG1238 159087013699 threonine dehydratase; Reviewed; Region: PRK09224 159087013700 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 159087013701 tetramer interface [polypeptide binding]; other site 159087013702 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087013703 catalytic residue [active] 159087013704 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 159087013705 putative Ile/Val binding site [chemical binding]; other site 159087013706 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 159087013707 putative Ile/Val binding site [chemical binding]; other site 159087013708 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 159087013709 AzlC protein; Region: AzlC; pfam03591 159087013710 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 159087013711 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 159087013712 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 159087013713 dimer interface [polypeptide binding]; other site 159087013714 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087013715 catalytic residue [active] 159087013716 putative C-S lyase; Region: C_S_lyase_PatB; TIGR04350 159087013717 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 159087013718 pyridoxal 5'-phosphate binding site [chemical binding]; other site 159087013719 homodimer interface [polypeptide binding]; other site 159087013720 catalytic residue [active] 159087013721 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 159087013722 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 159087013723 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 159087013724 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 159087013725 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 159087013726 N-acetyl-D-glucosamine binding site [chemical binding]; other site 159087013727 catalytic residue [active] 159087013728 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 159087013729 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 159087013730 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 159087013731 putative NAD(P) binding site [chemical binding]; other site 159087013732 active site 159087013733 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 159087013734 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 159087013735 active site 159087013736 NTP binding site [chemical binding]; other site 159087013737 metal binding triad [ion binding]; metal-binding site 159087013738 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 159087013739 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cl17503 159087013740 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 159087013741 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 159087013742 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 159087013743 PGAP1-like protein; Region: PGAP1; pfam07819 159087013744 Putative motility protein; Region: YjfB_motility; pfam14070 159087013745 Uncharacterized conserved protein [Function unknown]; Region: COG1565 159087013746 FIST N domain; Region: FIST; pfam08495 159087013747 Uncharacterized conserved protein [Function unknown]; Region: COG3287 159087013748 FIST C domain; Region: FIST_C; pfam10442 159087013749 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 159087013750 PAS domain; Region: PAS_9; pfam13426 159087013751 putative active site [active] 159087013752 heme pocket [chemical binding]; other site 159087013753 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 159087013754 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 159087013755 putative active site [active] 159087013756 heme pocket [chemical binding]; other site 159087013757 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 159087013758 dimer interface [polypeptide binding]; other site 159087013759 phosphorylation site [posttranslational modification] 159087013760 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 159087013761 ATP binding site [chemical binding]; other site 159087013762 Mg2+ binding site [ion binding]; other site 159087013763 G-X-G motif; other site 159087013764 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 159087013765 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 159087013766 active site 159087013767 phosphorylation site [posttranslational modification] 159087013768 intermolecular recognition site; other site 159087013769 dimerization interface [polypeptide binding]; other site 159087013770 Response regulator receiver domain; Region: Response_reg; pfam00072 159087013771 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 159087013772 active site 159087013773 phosphorylation site [posttranslational modification] 159087013774 intermolecular recognition site; other site 159087013775 dimerization interface [polypeptide binding]; other site 159087013776 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 159087013777 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 159087013778 Ligand Binding Site [chemical binding]; other site 159087013779 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 159087013780 cyclase homology domain; Region: CHD; cd07302 159087013781 nucleotidyl binding site; other site 159087013782 metal binding site [ion binding]; metal-binding site 159087013783 dimer interface [polypeptide binding]; other site 159087013784 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 159087013785 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 159087013786 phosphopeptide binding site; other site 159087013787 HPr kinase/phosphorylase; Provisional; Region: PRK05428 159087013788 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 159087013789 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 159087013790 Hpr binding site; other site 159087013791 active site 159087013792 homohexamer subunit interaction site [polypeptide binding]; other site 159087013793 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 159087013794 active site 159087013795 phosphorylation site [posttranslational modification] 159087013796 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 159087013797 30S subunit binding site; other site 159087013798 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 159087013799 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 159087013800 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 159087013801 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 159087013802 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 159087013803 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 159087013804 Walker A/P-loop; other site 159087013805 ATP binding site [chemical binding]; other site 159087013806 Q-loop/lid; other site 159087013807 ABC transporter signature motif; other site 159087013808 Walker B; other site 159087013809 D-loop; other site 159087013810 H-loop/switch region; other site 159087013811 recombination regulator RecX; Reviewed; Region: recX; PRK00117 159087013812 recombinase A; Provisional; Region: recA; PRK09354 159087013813 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 159087013814 hexamer interface [polypeptide binding]; other site 159087013815 Walker A motif; other site 159087013816 ATP binding site [chemical binding]; other site 159087013817 Walker B motif; other site 159087013818 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 159087013819 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 159087013820 active site 159087013821 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 159087013822 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 159087013823 Na binding site [ion binding]; other site 159087013824 putative glycosylation site [posttranslational modification]; other site 159087013825 putative glycosylation site [posttranslational modification]; other site 159087013826 VanZ like family; Region: VanZ; cl01971 159087013827 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 159087013828 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 159087013829 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 159087013830 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 159087013831 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 159087013832 motif II; other site 159087013833 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 159087013834 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 159087013835 dimer interface [polypeptide binding]; other site 159087013836 [2Fe-2S] cluster binding site [ion binding]; other site 159087013837 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 159087013838 nodulation ABC transporter NodI; Provisional; Region: PRK13537 159087013839 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 159087013840 Walker A/P-loop; other site 159087013841 ATP binding site [chemical binding]; other site 159087013842 Q-loop/lid; other site 159087013843 ABC transporter signature motif; other site 159087013844 Walker B; other site 159087013845 D-loop; other site 159087013846 H-loop/switch region; other site 159087013847 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 159087013848 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 159087013849 active site 159087013850 motif I; other site 159087013851 motif II; other site 159087013852 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 159087013853 2-phosphosulpholactate phosphatase; Region: 2-ph_phosp; pfam04029 159087013854 B12 binding domain; Region: B12-binding; pfam02310 159087013855 B12 binding site [chemical binding]; other site 159087013856 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 159087013857 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 159087013858 FeS/SAM binding site; other site 159087013859 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 159087013860 HDOD domain; Region: HDOD; pfam08668 159087013861 ABC-2 type transporter; Region: ABC2_membrane; cl17235 159087013862 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 159087013863 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 159087013864 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 159087013865 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 159087013866 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 159087013867 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 159087013868 DsbD alpha interface [polypeptide binding]; other site 159087013869 catalytic residues [active] 159087013870 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 159087013871 active site 159087013872 Phosphopantetheine attachment site; Region: PP-binding; cl09936 159087013873 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 159087013874 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 159087013875 dimer interface [polypeptide binding]; other site 159087013876 active site 159087013877 acyl carrier protein; Provisional; Region: PRK09184 159087013878 Predicted membrane protein [Function unknown]; Region: COG4648 159087013879 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087013880 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 159087013881 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 159087013882 acyl-activating enzyme (AAE) consensus motif; other site 159087013883 acyl-activating enzyme (AAE) consensus motif; other site 159087013884 AMP binding site [chemical binding]; other site 159087013885 active site 159087013886 CoA binding site [chemical binding]; other site 159087013887 FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation; Region: FabA_FabZ; cd00493 159087013888 active site 2 [active] 159087013889 dimer interface [polypeptide binding]; other site 159087013890 active site 1 [active] 159087013891 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 159087013892 putative acyl-acceptor binding pocket; other site 159087013893 Predicted exporter [General function prediction only]; Region: COG4258 159087013894 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 159087013895 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 159087013896 active site 159087013897 catalytic site [active] 159087013898 NodB motif; other site 159087013899 metal binding site [ion binding]; metal-binding site 159087013900 Methyltransferase domain; Region: Methyltransf_31; pfam13847 159087013901 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 159087013902 S-adenosylmethionine binding site [chemical binding]; other site 159087013903 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 159087013904 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 159087013905 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK12489 159087013906 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 159087013907 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 159087013908 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 159087013909 putative ligand binding site [chemical binding]; other site 159087013910 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 159087013911 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 159087013912 dimer interface [polypeptide binding]; other site 159087013913 active site 159087013914 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 159087013915 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 159087013916 putative active site 1 [active] 159087013917 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 159087013918 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 159087013919 NAD(P) binding site [chemical binding]; other site 159087013920 active site 159087013921 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 159087013922 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 159087013923 catalytic residues [active] 159087013924 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 159087013925 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 159087013926 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 159087013927 HPP family; Region: HPP; pfam04982 159087013928 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 159087013929 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 159087013930 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 159087013931 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 159087013932 Ligand binding site; other site 159087013933 Putative Catalytic site; other site 159087013934 DXD motif; other site 159087013935 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 159087013936 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 159087013937 putative acyl-acceptor binding pocket; other site 159087013938 MltA-interacting protein MipA; Region: MipA; cl01504 159087013939 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_5; cd06153 159087013940 homotrimer interaction site [polypeptide binding]; other site 159087013941 putative active site [active] 159087013942 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 159087013943 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 159087013944 magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase; Region: BchE; TIGR02026 159087013945 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 159087013946 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 159087013947 FeS/SAM binding site; other site 159087013948 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 159087013949 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 159087013950 trmE is a tRNA modification GTPase; Region: trmE; cd04164 159087013951 G1 box; other site 159087013952 GTP/Mg2+ binding site [chemical binding]; other site 159087013953 Switch I region; other site 159087013954 G2 box; other site 159087013955 Switch II region; other site 159087013956 G3 box; other site 159087013957 G4 box; other site 159087013958 G5 box; other site 159087013959 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 159087013960 membrane protein insertase; Provisional; Region: PRK01318 159087013961 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 159087013962 Haemolytic domain; Region: Haemolytic; pfam01809 159087013963 Ribonuclease P; Region: Ribonuclease_P; cl00457 159087013964 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399