-- dump date 20140619_001350 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1184267000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1184267000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1184267000003 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 1184267000004 Walker A motif; other site 1184267000005 ATP binding site [chemical binding]; other site 1184267000006 Walker B motif; other site 1184267000007 arginine finger; other site 1184267000008 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 1184267000009 DnaA box-binding interface [nucleotide binding]; other site 1184267000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 1184267000011 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 1184267000012 putative DNA binding surface [nucleotide binding]; other site 1184267000013 dimer interface [polypeptide binding]; other site 1184267000014 beta-clamp/clamp loader binding surface; other site 1184267000015 beta-clamp/translesion DNA polymerase binding surface; other site 1184267000016 recombination protein F; Reviewed; Region: recF; PRK00064 1184267000017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267000018 Walker A/P-loop; other site 1184267000019 ATP binding site [chemical binding]; other site 1184267000020 Q-loop/lid; other site 1184267000021 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267000022 ABC transporter signature motif; other site 1184267000023 Walker B; other site 1184267000024 D-loop; other site 1184267000025 H-loop/switch region; other site 1184267000026 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1184267000027 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 1184267000028 ATP binding site [chemical binding]; other site 1184267000029 Mg2+ binding site [ion binding]; other site 1184267000030 G-X-G motif; other site 1184267000031 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 1184267000032 anchoring element; other site 1184267000033 dimer interface [polypeptide binding]; other site 1184267000034 ATP binding site [chemical binding]; other site 1184267000035 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 1184267000036 active site 1184267000037 putative metal-binding site [ion binding]; other site 1184267000038 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1184267000039 DNA gyrase subunit A; Validated; Region: PRK05560 1184267000040 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 1184267000041 CAP-like domain; other site 1184267000042 active site 1184267000043 primary dimer interface [polypeptide binding]; other site 1184267000044 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1184267000045 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1184267000046 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1184267000047 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1184267000048 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1184267000049 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1184267000050 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 1184267000051 ATP synthase subunit C; Region: ATP-synt_C; cl00466 1184267000052 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1184267000053 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 1184267000054 active site 1184267000055 substrate binding site [chemical binding]; other site 1184267000056 metal binding site [ion binding]; metal-binding site 1184267000057 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 1184267000058 SurA N-terminal domain; Region: SurA_N; pfam09312 1184267000059 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1184267000060 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1184267000061 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1184267000062 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 1184267000063 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1184267000064 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 1184267000065 putative acyl-acceptor binding pocket; other site 1184267000066 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 1184267000067 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 1184267000068 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 1184267000069 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 1184267000070 Ligand binding site [chemical binding]; other site 1184267000071 Electron transfer flavoprotein domain; Region: ETF; pfam01012 1184267000072 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 1184267000073 Succinate:quinone oxidoreductase (SQR)-like Type B subfamily 2, transmembrane subunit; composed of proteins with similarity to the SQRs of Geobacter metallireducens and Corynebacterium glutamicum. SQR catalyzes the oxidation of succinate to fumarate...; Region: SQR_TypeB_2_TM; cd03498 1184267000074 putative Iron-sulfur protein interface [polypeptide binding]; other site 1184267000075 proximal heme binding site [chemical binding]; other site 1184267000076 distal heme binding site [chemical binding]; other site 1184267000077 putative dimer interface [polypeptide binding]; other site 1184267000078 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07573 1184267000079 L-aspartate oxidase; Provisional; Region: PRK06175 1184267000080 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1184267000081 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated; Region: PRK07570 1184267000082 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1184267000083 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1184267000084 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1184267000085 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 1184267000086 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 1184267000087 putative DNA binding site [nucleotide binding]; other site 1184267000088 putative Zn2+ binding site [ion binding]; other site 1184267000089 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267000090 catalytic triad [active] 1184267000091 putative active site [active] 1184267000092 CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast; Region: CUB; cd00041 1184267000093 heterodimerization interface [polypeptide binding]; other site 1184267000094 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1184267000095 Ribosomal protein S6; Region: Ribosomal_S6; pfam01250 1184267000096 Predicted membrane protein (DUF2232); Region: DUF2232; cl01728 1184267000097 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1184267000098 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1184267000099 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1184267000100 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 1184267000101 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1184267000102 catalytic residues [active] 1184267000103 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 1184267000104 TPR motif; other site 1184267000105 binding surface 1184267000106 TIGR02147 family protein; Region: Fsuc_second 1184267000107 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 1184267000108 Ligand Binding Site [chemical binding]; other site 1184267000109 NAD+ synthetase; Region: nadE; TIGR00552 1184267000110 Protein of unknown function (DUF4255); Region: DUF4255; pfam14065 1184267000111 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 1184267000112 non-specific DNA binding site [nucleotide binding]; other site 1184267000113 salt bridge; other site 1184267000114 sequence-specific DNA binding site [nucleotide binding]; other site 1184267000115 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 1184267000116 Catalytic site [active] 1184267000117 Thrombospondin type 1 repeats; Region: TSP1; smart00209 1184267000118 TM2 domain; Region: TM2; cl00984 1184267000119 TM2 domain; Region: TM2; cl00984 1184267000120 Thrombospondin type 1 repeats; Region: TSP1; smart00209 1184267000121 Thrombospondin type 1 repeats; Region: TSP1; smart00209 1184267000122 Thrombospondin type 1 repeats; Region: TSP1; smart00209 1184267000123 replicative DNA helicase; Region: DnaB; TIGR00665 1184267000124 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1184267000125 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 1184267000126 Walker A motif; other site 1184267000127 ATP binding site [chemical binding]; other site 1184267000128 Walker B motif; other site 1184267000129 DNA binding loops [nucleotide binding] 1184267000130 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 1184267000131 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 1184267000132 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 1184267000133 FeS/SAM binding site; other site 1184267000134 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1184267000135 Protein of unknown function (DUF497); Region: DUF497; cl01108 1184267000136 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1184267000137 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 1184267000138 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1184267000139 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 1184267000140 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 1184267000141 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 1184267000142 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1184267000143 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1184267000144 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 1184267000145 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1184267000146 dimer interface [polypeptide binding]; other site 1184267000147 active site 1184267000148 catalytic residue [active] 1184267000149 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1184267000150 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1184267000151 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1184267000152 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 1184267000153 active site 1184267000154 intersubunit interactions; other site 1184267000155 catalytic residue [active] 1184267000156 salt bridge; other site 1184267000157 non-specific DNA binding site [nucleotide binding]; other site 1184267000158 Helix-turn-helix domain; Region: HTH_37; pfam13744 1184267000159 sequence-specific DNA binding site [nucleotide binding]; other site 1184267000160 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 1184267000161 UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]; Region: MurD; COG0771 1184267000162 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1184267000163 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1184267000164 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 1184267000165 putative active site [active] 1184267000166 putative metal binding site [ion binding]; other site 1184267000167 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1184267000168 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1184267000169 ligand binding site [chemical binding]; other site 1184267000170 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1184267000171 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 1184267000172 nucleotide binding pocket [chemical binding]; other site 1184267000173 K-X-D-G motif; other site 1184267000174 catalytic site [active] 1184267000175 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1184267000176 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1184267000177 BRCA1 C Terminus (BRCT) domain; Region: BRCT; pfam00533 1184267000178 Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit [Translation, ribosomal structure and biogenesis]; Region: GatC; COG0721 1184267000179 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1184267000180 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1184267000181 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1184267000182 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1184267000183 GatB domain; Region: GatB_Yqey; smart00845 1184267000184 exopolyphosphatase; Region: exo_poly_only; TIGR03706 1184267000185 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1184267000186 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 1184267000187 PilZ domain; Region: PilZ; pfam07238 1184267000188 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1184267000189 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1184267000190 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 1184267000191 RNA binding site [nucleotide binding]; other site 1184267000192 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 1184267000193 multimer interface [polypeptide binding]; other site 1184267000194 Walker A motif; other site 1184267000195 ATP binding site [chemical binding]; other site 1184267000196 Walker B motif; other site 1184267000197 RDD family; Region: RDD; pfam06271 1184267000198 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 1184267000199 NADH(P)-binding; Region: NAD_binding_10; pfam13460 1184267000200 NAD binding site [chemical binding]; other site 1184267000201 active site 1184267000202 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 1184267000203 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1184267000204 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1184267000205 RF-1 domain; Region: RF-1; pfam00472 1184267000206 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 1184267000207 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 1184267000208 S-adenosylmethionine binding site [chemical binding]; other site 1184267000209 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1184267000210 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 1184267000211 hinge; other site 1184267000212 active site 1184267000213 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 1184267000214 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 1184267000215 binding surface 1184267000216 TPR motif; other site 1184267000217 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 1184267000218 binding surface 1184267000219 TPR motif; other site 1184267000220 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 1184267000221 binding surface 1184267000222 TPR motif; other site 1184267000223 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 1184267000224 binding surface 1184267000225 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1184267000226 TPR motif; other site 1184267000227 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 1184267000228 TPR motif; other site 1184267000229 binding surface 1184267000230 TPR repeat; Region: TPR_11; pfam13414 1184267000231 seryl-tRNA synthetase; Provisional; Region: PRK05431 1184267000232 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1184267000233 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 1184267000234 dimer interface [polypeptide binding]; other site 1184267000235 active site 1184267000236 motif 1; other site 1184267000237 motif 2; other site 1184267000238 motif 3; other site 1184267000239 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 1184267000240 catalytic triad [active] 1184267000241 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1184267000242 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 1184267000243 non-specific DNA binding site [nucleotide binding]; other site 1184267000244 salt bridge; other site 1184267000245 sequence-specific DNA binding site [nucleotide binding]; other site 1184267000246 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 1184267000247 minor groove reading motif; other site 1184267000248 helix-hairpin-helix signature motif; other site 1184267000249 active site 1184267000250 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 1184267000251 sequence-specific DNA binding site [nucleotide binding]; other site 1184267000252 salt bridge; other site 1184267000253 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1184267000254 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 1184267000255 ATP binding site [chemical binding]; other site 1184267000256 substrate binding site [chemical binding]; other site 1184267000257 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; pfam05014 1184267000258 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 1184267000259 Ligand Binding Site [chemical binding]; other site 1184267000260 FMN binding site [chemical binding]; other site 1184267000261 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 1184267000262 dimer interface [polypeptide binding]; other site 1184267000263 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 1184267000264 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 1184267000265 TIGR02147 family protein; Region: Fsuc_second 1184267000266 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1184267000267 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 1184267000268 putative substrate translocation pore; other site 1184267000269 Fungal specific transcription factor domain; Region: Fungal_trans_2; pfam11951 1184267000270 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1184267000271 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 1184267000272 Uncharacterized conserved protein [Function unknown]; Region: COG3791 1184267000273 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1184267000274 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 1184267000275 putative dimer interface [polypeptide binding]; other site 1184267000276 Protein of unknown function DUF72; Region: DUF72; pfam01904 1184267000277 ZIP Zinc transporter; Region: Zip; pfam02535 1184267000278 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 1184267000279 Pirin-related protein [General function prediction only]; Region: COG1741 1184267000280 Pirin; Region: Pirin; pfam02678 1184267000281 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 1184267000282 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 1184267000283 S1/P1 nucleases and related enzymes; Region: S1-P1_nuclease; cd11010 1184267000284 active site 1184267000285 Zn binding site [ion binding]; other site 1184267000286 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 1184267000287 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1184267000288 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 1184267000289 RNA binding surface [nucleotide binding]; other site 1184267000290 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1184267000291 active site 1184267000292 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 1184267000293 HSP70 interaction site [polypeptide binding]; other site 1184267000294 Helix-turn-helix domain; Region: HTH_25; pfam13413 1184267000295 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 1184267000296 Glycoprotease family; Region: Peptidase_M22; pfam00814 1184267000297 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 1184267000298 active site 1184267000299 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 1184267000300 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 1184267000301 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 1184267000302 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 1184267000303 putative substrate binding region [chemical binding]; other site 1184267000304 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1184267000305 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1184267000306 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 1184267000307 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1184267000308 catalytic residue [active] 1184267000309 putative FPP diphosphate binding site; other site 1184267000310 putative FPP binding hydrophobic cleft; other site 1184267000311 dimer interface [polypeptide binding]; other site 1184267000312 putative IPP diphosphate binding site; other site 1184267000313 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1184267000314 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 1184267000315 hinge region; other site 1184267000316 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 1184267000317 putative nucleotide binding site [chemical binding]; other site 1184267000318 uridine monophosphate binding site [chemical binding]; other site 1184267000319 homohexameric interface [polypeptide binding]; other site 1184267000320 elongation factor Ts; Provisional; Region: tsf; PRK09377 1184267000321 UBA/TS-N domain; Region: UBA; pfam00627 1184267000322 Elongation factor TS; Region: EF_TS; pfam00889 1184267000323 Elongation factor TS; Region: EF_TS; pfam00889 1184267000324 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 1184267000325 rRNA interaction site [nucleotide binding]; other site 1184267000326 S8 interaction site; other site 1184267000327 putative laminin-1 binding site; other site 1184267000328 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 1184267000329 active site 1184267000330 substrate binding sites [chemical binding]; other site 1184267000331 primosome assembly protein PriA; Validated; Region: PRK05580 1184267000332 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 1184267000333 ATP binding site [chemical binding]; other site 1184267000334 putative Mg++ binding site [ion binding]; other site 1184267000335 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1184267000336 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1184267000337 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1184267000338 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 1184267000339 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 1184267000340 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 1184267000341 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 1184267000342 active site 1184267000343 Phosphotransferase enzyme family; Region: APH; pfam01636 1184267000344 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 1184267000345 substrate binding site [chemical binding]; other site 1184267000346 AAA domain; Region: AAA_22; pfam13401 1184267000347 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1184267000348 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 1184267000349 Walker A motif; other site 1184267000350 ATP binding site [chemical binding]; other site 1184267000351 Walker B motif; other site 1184267000352 arginine finger; other site 1184267000353 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267000354 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1184267000355 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1184267000356 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 1184267000357 Walker A/P-loop; other site 1184267000358 ATP binding site [chemical binding]; other site 1184267000359 Q-loop/lid; other site 1184267000360 ABC transporter signature motif; other site 1184267000361 Walker B; other site 1184267000362 D-loop; other site 1184267000363 H-loop/switch region; other site 1184267000364 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 1184267000365 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1184267000366 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1184267000367 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267000368 Walker A/P-loop; other site 1184267000369 ATP binding site [chemical binding]; other site 1184267000370 Q-loop/lid; other site 1184267000371 ABC transporter signature motif; other site 1184267000372 Walker B; other site 1184267000373 D-loop; other site 1184267000374 H-loop/switch region; other site 1184267000375 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1184267000376 Transglycosylase; Region: Transgly; pfam00912 1184267000377 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 1184267000378 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1184267000379 Benzoate membrane transport protein; Region: BenE; pfam03594 1184267000380 benzoate transporter; Region: benE; TIGR00843 1184267000381 MAPEG family; Region: MAPEG; cl09190 1184267000382 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 1184267000383 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 1184267000384 C-terminal domain interface [polypeptide binding]; other site 1184267000385 GSH binding site (G-site) [chemical binding]; other site 1184267000386 dimer interface [polypeptide binding]; other site 1184267000387 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 1184267000388 N-terminal domain interface [polypeptide binding]; other site 1184267000389 dimer interface [polypeptide binding]; other site 1184267000390 substrate binding pocket (H-site) [chemical binding]; other site 1184267000391 DNA alkylation repair enzyme [DNA replication, recombination, and repair]; Region: COG4335 1184267000392 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12647 1184267000393 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1184267000394 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 1184267000395 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1184267000396 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 1184267000397 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12663 1184267000398 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1184267000399 Na+/H+ ion antiporter subunit; Region: MNHE; pfam01899 1184267000400 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 1184267000401 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 1184267000402 Protein of unknown function (DUF1402); Region: DUF1402; pfam07182 1184267000403 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1184267000404 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1184267000405 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 1184267000406 DNA binding site [nucleotide binding] 1184267000407 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1184267000408 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1184267000409 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 1184267000410 Walker A motif; other site 1184267000411 ATP binding site [chemical binding]; other site 1184267000412 Walker B motif; other site 1184267000413 arginine finger; other site 1184267000414 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1184267000415 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1184267000416 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1184267000417 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1184267000418 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 1184267000419 Walker A motif; other site 1184267000420 ATP binding site [chemical binding]; other site 1184267000421 Walker B motif; other site 1184267000422 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1184267000423 Clp protease; Region: CLP_protease; pfam00574 1184267000424 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1184267000425 oligomer interface [polypeptide binding]; other site 1184267000426 active site residues [active] 1184267000427 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1184267000428 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 1184267000429 interface (dimer of trimers) [polypeptide binding]; other site 1184267000430 Substrate-binding/catalytic site; other site 1184267000431 Zn-binding sites [ion binding]; other site 1184267000432 Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Region: Endonuclease_V; cl00653 1184267000433 Glutamate-cysteine ligase; Region: GshA; pfam08886 1184267000434 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 1184267000435 Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: ArsA; COG0003 1184267000436 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 1184267000437 P loop; other site 1184267000438 Nucleotide binding site [chemical binding]; other site 1184267000439 DTAP/Switch II; other site 1184267000440 Switch I; other site 1184267000441 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 1184267000442 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 1184267000443 P loop; other site 1184267000444 Nucleotide binding site [chemical binding]; other site 1184267000445 DTAP/Switch II; other site 1184267000446 trigger factor; Region: tig; TIGR00115 1184267000447 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1184267000448 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1184267000449 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1184267000450 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1184267000451 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 1184267000452 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1184267000453 Catalytic dyad [active] 1184267000454 Peptidase family M23; Region: Peptidase_M23; pfam01551 1184267000455 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 1184267000456 FtsX-like permease family; Region: FtsX; pfam02687 1184267000457 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 1184267000458 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1184267000459 Walker A/P-loop; other site 1184267000460 ATP binding site [chemical binding]; other site 1184267000461 Q-loop/lid; other site 1184267000462 ABC transporter signature motif; other site 1184267000463 Walker B; other site 1184267000464 D-loop; other site 1184267000465 H-loop/switch region; other site 1184267000466 Protein of unknown function, DUF481; Region: DUF481; cl01213 1184267000467 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 1184267000468 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 1184267000469 Predicted membrane protein [Function unknown]; Region: COG3650 1184267000470 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1184267000471 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 1184267000472 Quinolinate synthetase A protein; Region: NadA; pfam02445 1184267000473 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1184267000474 GTPase SAR1 and related small G proteins [General function prediction only]; Region: COG1100 1184267000475 G3 box; other site 1184267000476 Switch II region; other site 1184267000477 GTP/Mg2+ binding site [chemical binding]; other site 1184267000478 G4 box; other site 1184267000479 G5 box; other site 1184267000480 recombination protein RecR; Reviewed; Region: recR; PRK00076 1184267000481 RecR protein; Region: RecR; pfam02132 1184267000482 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 1184267000483 putative active site [active] 1184267000484 putative metal-binding site [ion binding]; other site 1184267000485 tetramer interface [polypeptide binding]; other site 1184267000486 hypothetical protein; Validated; Region: PRK00153 1184267000487 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 1184267000488 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 1184267000489 Walker A motif; other site 1184267000490 ATP binding site [chemical binding]; other site 1184267000491 Walker B motif; other site 1184267000492 arginine finger; other site 1184267000493 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1184267000494 serine/threonine protein kinase; Provisional; Region: PRK11768 1184267000495 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 1184267000496 TIGR02147 family protein; Region: Fsuc_second 1184267000497 flagellar basal-body rod protein FlgC; Region: FlgC; TIGR01395 1184267000498 Domain of unknown function (DUF4423); Region: DUF4423; pfam14394 1184267000499 Peptidase family M48; Region: Peptidase_M48; cl12018 1184267000500 Helix-turn-helix XRE-family like proteins; Region: HTH_XRE; smart00530 1184267000501 sequence-specific DNA binding site [nucleotide binding]; other site 1184267000502 salt bridge; other site 1184267000503 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 1184267000504 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 1184267000505 active site 1184267000506 catalytic residues [active] 1184267000507 DNA binding site [nucleotide binding] 1184267000508 Int/Topo IB signature motif; other site 1184267000509 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1184267000510 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1184267000511 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 1184267000512 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 1184267000513 Walker A motif; other site 1184267000514 ATP binding site [chemical binding]; other site 1184267000515 Walker B motif; other site 1184267000516 arginine finger; other site 1184267000517 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 1184267000518 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 1184267000519 motif II; other site 1184267000520 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 1184267000521 DNA-binding interface [nucleotide binding]; DNA binding site 1184267000522 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1184267000523 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 1184267000524 ATP binding site [chemical binding]; other site 1184267000525 putative Mg++ binding site [ion binding]; other site 1184267000526 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 1184267000527 nucleotide binding region [chemical binding]; other site 1184267000528 ATP-binding site [chemical binding]; other site 1184267000529 EcoEI R protein C-terminal; Region: EcoEI_R_C; pfam08463 1184267000530 EcoKI restriction-modification system protein HsdS; Provisional; Region: PRK09737 1184267000531 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1184267000532 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1184267000533 Virulence protein [General function prediction only]; Region: COG3943 1184267000534 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 1184267000535 HsdM N-terminal domain; Region: HsdM_N; pfam12161 1184267000536 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 1184267000537 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 1184267000538 S-adenosylmethionine binding site [chemical binding]; other site 1184267000539 EF-hand domain pair; Region: EF_hand_5; pfam13499 1184267000540 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 1184267000541 Ca2+ binding site [ion binding]; other site 1184267000542 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 1184267000543 Ca2+ binding site [ion binding]; other site 1184267000544 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 1184267000545 non-specific DNA binding site [nucleotide binding]; other site 1184267000546 salt bridge; other site 1184267000547 sequence-specific DNA binding site [nucleotide binding]; other site 1184267000548 HipA N-terminal domain; Region: Couple_hipA; pfam13657 1184267000549 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 1184267000550 HipA-like N-terminal domain; Region: HipA_N; pfam07805 1184267000551 HipA-like C-terminal domain; Region: HipA_C; pfam07804 1184267000552 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 1184267000553 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 1184267000554 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1184267000555 Helix-turn-helix domain; Region: HTH_18; pfam12833 1184267000556 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1184267000557 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 1184267000558 classical (c) SDRs; Region: SDR_c; cd05233 1184267000559 NAD(P) binding site [chemical binding]; other site 1184267000560 active site 1184267000561 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 1184267000562 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 1184267000563 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 1184267000564 tetramer interface [polypeptide binding]; other site 1184267000565 heme binding pocket [chemical binding]; other site 1184267000566 NADPH binding site [chemical binding]; other site 1184267000567 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 1184267000568 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 1184267000569 FMN binding site [chemical binding]; other site 1184267000570 substrate binding site [chemical binding]; other site 1184267000571 putative catalytic residue [active] 1184267000572 Predicted membrane protein [Function unknown]; Region: COG4270 1184267000573 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 1184267000574 putative active site [active] 1184267000575 Zn binding site [ion binding]; other site 1184267000576 BON domain; Region: BON; pfam04972 1184267000577 BON domain; Region: BON; pfam04972 1184267000578 PAS fold; Region: PAS_4; pfam08448 1184267000579 PAS fold; Region: PAS_3; pfam08447 1184267000580 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 1184267000581 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267000582 PAS fold; Region: PAS_3; pfam08447 1184267000583 putative active site [active] 1184267000584 heme pocket [chemical binding]; other site 1184267000585 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 1184267000586 dimer interface [polypeptide binding]; other site 1184267000587 phosphorylation site [posttranslational modification] 1184267000588 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 1184267000589 ATP binding site [chemical binding]; other site 1184267000590 Mg2+ binding site [ion binding]; other site 1184267000591 G-X-G motif; other site 1184267000592 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1184267000593 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267000594 active site 1184267000595 phosphorylation site [posttranslational modification] 1184267000596 intermolecular recognition site; other site 1184267000597 dimerization interface [polypeptide binding]; other site 1184267000598 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1184267000599 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1184267000600 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1184267000601 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 1184267000602 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 1184267000603 ATP binding site [chemical binding]; other site 1184267000604 putative Mg++ binding site [ion binding]; other site 1184267000605 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 1184267000606 nucleotide binding region [chemical binding]; other site 1184267000607 ATP-binding site [chemical binding]; other site 1184267000608 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1184267000609 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1184267000610 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 1184267000611 TrkA-N domain; Region: TrkA_N; pfam02254 1184267000612 helicase 45; Provisional; Region: PTZ00424 1184267000613 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 1184267000614 ATP binding site [chemical binding]; other site 1184267000615 Mg++ binding site [ion binding]; other site 1184267000616 motif III; other site 1184267000617 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 1184267000618 nucleotide binding region [chemical binding]; other site 1184267000619 ATP-binding site [chemical binding]; other site 1184267000620 Protein of unknown function (DUF461); Region: DUF461; pfam04314 1184267000621 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1184267000622 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 1184267000623 Cu(I) binding site [ion binding]; other site 1184267000624 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1184267000625 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1184267000626 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267000627 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267000628 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 1184267000629 dimerization interface [polypeptide binding]; other site 1184267000630 substrate binding pocket [chemical binding]; other site 1184267000631 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1184267000632 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 1184267000633 active site 1184267000634 catalytic residues [active] 1184267000635 metal binding site [ion binding]; metal-binding site 1184267000636 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267000637 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267000638 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 1184267000639 putative effector binding pocket; other site 1184267000640 dimerization interface [polypeptide binding]; other site 1184267000641 Uncharacterized conserved protein [Function unknown]; Region: COG2353 1184267000642 Pirin-related protein [General function prediction only]; Region: COG1741 1184267000643 Pirin; Region: Pirin; pfam02678 1184267000644 topology modulation protein; Provisional; Region: PRK07261 1184267000645 AAA domain; Region: AAA_17; pfam13207 1184267000646 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 1184267000647 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 1184267000648 PhnA protein; Region: PhnA; pfam03831 1184267000649 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 1184267000650 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 1184267000651 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 1184267000652 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1184267000653 ligand binding site [chemical binding]; other site 1184267000654 flexible hinge region; other site 1184267000655 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 1184267000656 non-specific DNA interactions [nucleotide binding]; other site 1184267000657 DNA binding site [nucleotide binding] 1184267000658 sequence specific DNA binding site [nucleotide binding]; other site 1184267000659 putative cAMP binding site [chemical binding]; other site 1184267000660 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 1184267000661 active site residue [active] 1184267000662 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 1184267000663 active site residue [active] 1184267000664 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 1184267000665 Predicted transporter component [General function prediction only]; Region: COG2391 1184267000666 Predicted transporter component [General function prediction only]; Region: COG2391 1184267000667 Sulphur transport; Region: Sulf_transp; pfam04143 1184267000668 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1184267000669 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 1184267000670 putative metal binding site [ion binding]; other site 1184267000671 putative homodimer interface [polypeptide binding]; other site 1184267000672 putative homotetramer interface [polypeptide binding]; other site 1184267000673 putative homodimer-homodimer interface [polypeptide binding]; other site 1184267000674 putative allosteric switch controlling residues; other site 1184267000675 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 1184267000676 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 1184267000677 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 1184267000678 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267000679 Zn2+ binding site [ion binding]; other site 1184267000680 Mg2+ binding site [ion binding]; other site 1184267000681 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1184267000682 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267000683 Walker A/P-loop; other site 1184267000684 ATP binding site [chemical binding]; other site 1184267000685 Q-loop/lid; other site 1184267000686 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267000687 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267000688 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 1184267000689 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1184267000690 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1184267000691 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1184267000692 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267000693 putative active site [active] 1184267000694 catalytic triad [active] 1184267000695 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 1184267000696 catalytic residues [active] 1184267000697 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 1184267000698 Interdomain contacts; other site 1184267000699 Cytokine receptor motif; other site 1184267000700 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 1184267000701 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1184267000702 nucleotide binding site [chemical binding]; other site 1184267000703 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 1184267000704 Ca2+ binding site [ion binding]; other site 1184267000705 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_1; cd07818 1184267000706 putative hydrophobic ligand binding site [chemical binding]; other site 1184267000707 GyrI-like small molecule binding domain; Region: GyrI-like; pfam06445 1184267000708 TfoX C-terminal domain; Region: TfoX_C; pfam04994 1184267000709 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 1184267000710 Chlamydia CHLPS protein (DUF818); Region: DUF818; pfam05677 1184267000711 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 1184267000712 TAP-like protein; Region: Abhydrolase_4; pfam08386 1184267000713 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267000714 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267000715 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 1184267000716 putative effector binding pocket; other site 1184267000717 dimerization interface [polypeptide binding]; other site 1184267000718 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 1184267000719 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 1184267000720 NADP binding site [chemical binding]; other site 1184267000721 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_5; cd02148 1184267000722 putative FMN binding site [chemical binding]; other site 1184267000723 FOG: CBS domain [General function prediction only]; Region: COG0517 1184267000724 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 1184267000725 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 1184267000726 active site clefts [active] 1184267000727 zinc binding site [ion binding]; other site 1184267000728 dimer interface [polypeptide binding]; other site 1184267000729 Uncharacterized conserved protein [Function unknown]; Region: COG3791 1184267000730 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1184267000731 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1184267000732 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 1184267000733 homodimer interface [polypeptide binding]; other site 1184267000734 chemical substrate binding site [chemical binding]; other site 1184267000735 oligomer interface [polypeptide binding]; other site 1184267000736 metal binding site [ion binding]; metal-binding site 1184267000737 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 1184267000738 anti sigma factor interaction site; other site 1184267000739 regulatory phosphorylation site [posttranslational modification]; other site 1184267000740 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 1184267000741 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 1184267000742 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 1184267000743 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 1184267000744 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267000745 active site 1184267000746 phosphorylation site [posttranslational modification] 1184267000747 intermolecular recognition site; other site 1184267000748 dimerization interface [polypeptide binding]; other site 1184267000749 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 1184267000750 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 1184267000751 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267000752 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267000753 active site 1184267000754 phosphorylation site [posttranslational modification] 1184267000755 intermolecular recognition site; other site 1184267000756 dimerization interface [polypeptide binding]; other site 1184267000757 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 1184267000758 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267000759 active site 1184267000760 phosphorylation site [posttranslational modification] 1184267000761 intermolecular recognition site; other site 1184267000762 dimerization interface [polypeptide binding]; other site 1184267000763 CheB methylesterase; Region: CheB_methylest; pfam01339 1184267000764 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1184267000765 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267000766 putative active site [active] 1184267000767 heme pocket [chemical binding]; other site 1184267000768 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267000769 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1184267000770 putative active site [active] 1184267000771 heme pocket [chemical binding]; other site 1184267000772 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1184267000773 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1184267000774 dimer interface [polypeptide binding]; other site 1184267000775 putative CheW interface [polypeptide binding]; other site 1184267000776 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 1184267000777 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 1184267000778 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1184267000779 putative binding surface; other site 1184267000780 active site 1184267000781 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 1184267000782 putative binding surface; other site 1184267000783 active site 1184267000784 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 1184267000785 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 1184267000786 ATP binding site [chemical binding]; other site 1184267000787 Mg2+ binding site [ion binding]; other site 1184267000788 G-X-G motif; other site 1184267000789 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 1184267000790 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 1184267000791 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267000792 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267000793 active site 1184267000794 phosphorylation site [posttranslational modification] 1184267000795 intermolecular recognition site; other site 1184267000796 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 1184267000797 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 1184267000798 active site 1184267000799 DNA binding site [nucleotide binding] 1184267000800 Predicted membrane protein [Function unknown]; Region: COG2259 1184267000801 Pirin-related protein [General function prediction only]; Region: COG1741 1184267000802 Pirin; Region: Pirin; pfam02678 1184267000803 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 1184267000804 Protein of unknown function (DUF808); Region: DUF808; pfam05661 1184267000805 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 1184267000806 active site 2 [active] 1184267000807 active site 1 [active] 1184267000808 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 1184267000809 active site 2 [active] 1184267000810 active site 1 [active] 1184267000811 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1184267000812 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 1184267000813 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 1184267000814 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 1184267000815 FAD binding pocket [chemical binding]; other site 1184267000816 FAD binding motif [chemical binding]; other site 1184267000817 phosphate binding motif [ion binding]; other site 1184267000818 NAD binding pocket [chemical binding]; other site 1184267000819 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 1184267000820 catalytic core [active] 1184267000821 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1184267000822 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1184267000823 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1184267000824 AlkA N-terminal domain; Region: AlkA_N; pfam06029 1184267000825 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 1184267000826 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1184267000827 minor groove reading motif; other site 1184267000828 helix-hairpin-helix signature motif; other site 1184267000829 substrate binding pocket [chemical binding]; other site 1184267000830 active site 1184267000831 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 1184267000832 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1184267000833 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 1184267000834 DNA binding site [nucleotide binding] 1184267000835 active site 1184267000836 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 1184267000837 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 1184267000838 catalytic residues [active] 1184267000839 Peptidase family M48; Region: Peptidase_M48; cl12018 1184267000840 Outer membrane efflux protein; Region: OEP; pfam02321 1184267000841 Outer membrane efflux protein; Region: OEP; pfam02321 1184267000842 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1184267000843 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 1184267000844 probable F420-dependent oxidoreductase, MSMEG_4141 family; Region: F420_MSMEG_4141; TIGR03620 1184267000845 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 1184267000846 aconitate hydratase; Validated; Region: PRK09277 1184267000847 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1184267000848 substrate binding site [chemical binding]; other site 1184267000849 ligand binding site [chemical binding]; other site 1184267000850 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 1184267000851 substrate binding site [chemical binding]; other site 1184267000852 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 1184267000853 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1184267000854 catalytic residue [active] 1184267000855 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 1184267000856 ATP binding site [chemical binding]; other site 1184267000857 substrate interface [chemical binding]; other site 1184267000858 V4R domain; Region: V4R; cl15268 1184267000859 Domain of unknown function DUF21; Region: DUF21; pfam01595 1184267000860 FOG: CBS domain [General function prediction only]; Region: COG0517 1184267000861 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 1184267000862 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1184267000863 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 1184267000864 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 1184267000865 FeS/SAM binding site; other site 1184267000866 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1184267000867 PLD-like domain; Region: PLDc_2; pfam13091 1184267000868 putative active site [active] 1184267000869 catalytic site [active] 1184267000870 PLD-like domain; Region: PLDc_2; pfam13091 1184267000871 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1184267000872 putative active site [active] 1184267000873 catalytic site [active] 1184267000874 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1184267000875 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1184267000876 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1184267000877 hypothetical protein; Provisional; Region: PRK02250 1184267000878 mce related protein; Region: MCE; pfam02470 1184267000879 mce related protein; Region: MCE; pfam02470 1184267000880 Paraquat-inducible protein A; Region: PqiA; pfam04403 1184267000881 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1184267000882 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 1184267000883 iron-sulfur cluster [ion binding]; other site 1184267000884 [2Fe-2S] cluster binding site [ion binding]; other site 1184267000885 Uncharacterized stress protein (general stress protein 26) [General function prediction only]; Region: COG3871 1184267000886 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 1184267000887 BON domain; Region: BON; pfam04972 1184267000888 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267000889 putative catalytic site [active] 1184267000890 putative metal binding site [ion binding]; other site 1184267000891 putative phosphate binding site [ion binding]; other site 1184267000892 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 1184267000893 PLD-like domain; Region: PLDc_2; pfam13091 1184267000894 putative active site [active] 1184267000895 catalytic site [active] 1184267000896 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 1184267000897 PLD-like domain; Region: PLDc_2; pfam13091 1184267000898 putative active site [active] 1184267000899 catalytic site [active] 1184267000900 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 1184267000901 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 1184267000902 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; pfam09982 1184267000903 Ferritin-like domain; Region: Ferritin; pfam00210 1184267000904 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 1184267000905 dinuclear metal binding motif [ion binding]; other site 1184267000906 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 1184267000907 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 1184267000908 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 1184267000909 CsbD-like; Region: CsbD; pfam05532 1184267000910 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1184267000911 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267000912 active site 1184267000913 phosphorylation site [posttranslational modification] 1184267000914 intermolecular recognition site; other site 1184267000915 dimerization interface [polypeptide binding]; other site 1184267000916 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 1184267000917 Walker A motif; other site 1184267000918 ATP binding site [chemical binding]; other site 1184267000919 Walker B motif; other site 1184267000920 arginine finger; other site 1184267000921 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267000922 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1184267000923 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1184267000924 ligand binding site [chemical binding]; other site 1184267000925 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 1184267000926 methionine sulfoxide reductase B; Provisional; Region: PRK00222 1184267000927 SelR domain; Region: SelR; pfam01641 1184267000928 ABC-2 type transporter; Region: ABC2_membrane; cl17235 1184267000929 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 1184267000930 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1184267000931 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 1184267000932 Walker A/P-loop; other site 1184267000933 ATP binding site [chemical binding]; other site 1184267000934 Q-loop/lid; other site 1184267000935 ABC transporter signature motif; other site 1184267000936 Walker B; other site 1184267000937 D-loop; other site 1184267000938 H-loop/switch region; other site 1184267000939 Predicted membrane protein [Function unknown]; Region: COG2261 1184267000940 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 1184267000941 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1184267000942 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3214 1184267000943 Protein of unknown function (DUF1006); Region: DUF1006; pfam06224 1184267000944 rod shape-determining protein MreB; Provisional; Region: PRK13927 1184267000945 MreB and similar proteins; Region: MreB_like; cd10225 1184267000946 nucleotide binding site [chemical binding]; other site 1184267000947 Mg binding site [ion binding]; other site 1184267000948 putative protofilament interaction site [polypeptide binding]; other site 1184267000949 RodZ interaction site [polypeptide binding]; other site 1184267000950 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 1184267000951 dimerization interface [polypeptide binding]; other site 1184267000952 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 1184267000953 dimer interface [polypeptide binding]; other site 1184267000954 phosphorylation site [posttranslational modification] 1184267000955 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 1184267000956 ATP binding site [chemical binding]; other site 1184267000957 Mg2+ binding site [ion binding]; other site 1184267000958 G-X-G motif; other site 1184267000959 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1184267000960 MPN+ (JAMM) motif; other site 1184267000961 Zinc-binding site [ion binding]; other site 1184267000962 Protein of unknown function (DUF3897); Region: DUF3897; pfam13036 1184267000963 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 1184267000964 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 1184267000965 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 1184267000966 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 1184267000967 TPR motif; other site 1184267000968 binding surface 1184267000969 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 1184267000970 binding surface 1184267000971 TPR motif; other site 1184267000972 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1184267000973 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 1184267000974 binding surface 1184267000975 TPR motif; other site 1184267000976 PrkA AAA domain; Region: AAA_PrkA; smart00763 1184267000977 AAA ATPase domain; Region: AAA_16; pfam13191 1184267000978 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 1184267000979 hypothetical protein; Provisional; Region: PRK05325 1184267000980 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 1184267000981 SpoVR like protein; Region: SpoVR; pfam04293 1184267000982 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 1184267000983 putative rRNA binding site [nucleotide binding]; other site 1184267000984 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1184267000985 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267000986 active site 1184267000987 phosphorylation site [posttranslational modification] 1184267000988 intermolecular recognition site; other site 1184267000989 dimerization interface [polypeptide binding]; other site 1184267000990 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 1184267000991 DNA binding site [nucleotide binding] 1184267000992 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 1184267000993 S-adenosylmethionine binding site [chemical binding]; other site 1184267000994 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 1184267000995 nucleoside/Zn binding site; other site 1184267000996 dimer interface [polypeptide binding]; other site 1184267000997 catalytic motif [active] 1184267000998 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 1184267000999 Yqey-like protein; Region: YqeY; pfam09424 1184267001000 DNA primase, catalytic core; Region: dnaG; TIGR01391 1184267001001 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1184267001002 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1184267001003 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 1184267001004 active site 1184267001005 metal binding site [ion binding]; metal-binding site 1184267001006 interdomain interaction site; other site 1184267001007 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 1184267001008 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1184267001009 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1184267001010 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1184267001011 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1184267001012 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1184267001013 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 1184267001014 DNA binding residues [nucleotide binding] 1184267001015 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 1184267001016 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 1184267001017 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 1184267001018 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 1184267001019 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 1184267001020 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1184267001021 EamA-like transporter family; Region: EamA; pfam00892 1184267001022 methionine sulfoxide reductase B; Provisional; Region: PRK00222 1184267001023 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 1184267001024 methionine sulfoxide reductase A; Provisional; Region: PRK14054 1184267001025 Protein of unknown function (DUF962); Region: DUF962; pfam06127 1184267001026 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267001027 catalytic triad [active] 1184267001028 putative active site [active] 1184267001029 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1184267001030 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1184267001031 metal binding site [ion binding]; metal-binding site 1184267001032 active site 1184267001033 I-site; other site 1184267001034 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267001035 catalytic triad [active] 1184267001036 putative active site [active] 1184267001037 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1184267001038 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1184267001039 metal binding site [ion binding]; metal-binding site 1184267001040 active site 1184267001041 I-site; other site 1184267001042 Protein of unknown function (DUF1653); Region: DUF1653; pfam07866 1184267001043 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 1184267001044 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1184267001045 Coenzyme A binding pocket [chemical binding]; other site 1184267001046 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 1184267001047 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 1184267001048 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1184267001049 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 1184267001050 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1184267001051 Coenzyme A binding pocket [chemical binding]; other site 1184267001052 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 1184267001053 lipoyl attachment site [posttranslational modification]; other site 1184267001054 FOG: Glucan-binding domain (YG repeat) [General function prediction only]; Region: COG5263 1184267001055 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 1184267001056 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1184267001057 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 1184267001058 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1184267001059 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 1184267001060 nucleotide binding region [chemical binding]; other site 1184267001061 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1184267001062 Cytochrome c; Region: Cytochrom_C; pfam00034 1184267001063 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 1184267001064 Cu(I) binding site [ion binding]; other site 1184267001065 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 1184267001066 ER lumen protein retaining receptor; Region: ER_lumen_recept; cl02155 1184267001067 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1184267001068 Cytochrome c; Region: Cytochrom_C; pfam00034 1184267001069 cytochrome c oxidase, subunit I; Region: CtaD_CoxA; TIGR02891 1184267001070 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 1184267001071 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 1184267001072 Subunit I/III interface [polypeptide binding]; other site 1184267001073 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 1184267001074 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 1184267001075 UbiA prenyltransferase family; Region: UbiA; pfam01040 1184267001076 maleylacetoacetate isomerase; Region: maiA; TIGR01262 1184267001077 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 1184267001078 C-terminal domain interface [polypeptide binding]; other site 1184267001079 GSH binding site (G-site) [chemical binding]; other site 1184267001080 putative dimer interface [polypeptide binding]; other site 1184267001081 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 1184267001082 dimer interface [polypeptide binding]; other site 1184267001083 N-terminal domain interface [polypeptide binding]; other site 1184267001084 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 1184267001085 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 1184267001086 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 1184267001087 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 1184267001088 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 1184267001089 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267001090 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267001091 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 1184267001092 dimerization interface [polypeptide binding]; other site 1184267001093 OsmC-like protein; Region: OsmC; pfam02566 1184267001094 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1184267001095 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 1184267001096 Walker A motif; other site 1184267001097 ATP binding site [chemical binding]; other site 1184267001098 Walker B motif; other site 1184267001099 arginine finger; other site 1184267001100 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1184267001101 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 1184267001102 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1184267001103 LexA repressor; Validated; Region: PRK00215 1184267001104 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 1184267001105 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 1184267001106 Catalytic site [active] 1184267001107 Peptidase M14-like domain of Escherichia coli Murein Peptide Amidase A and related proteins; Region: M14_MpaA_like; cd06904 1184267001108 putative active site [active] 1184267001109 Zn binding site [ion binding]; other site 1184267001110 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 1184267001111 ligand binding site [chemical binding]; other site 1184267001112 active site 1184267001113 UGI interface [polypeptide binding]; other site 1184267001114 catalytic site [active] 1184267001115 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1184267001116 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267001117 ABC transporter; Region: ABC_tran_2; pfam12848 1184267001118 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267001119 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1184267001120 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 1184267001121 peptide binding site [polypeptide binding]; other site 1184267001122 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1184267001123 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 1184267001124 dimer interface [polypeptide binding]; other site 1184267001125 conserved gate region; other site 1184267001126 putative PBP binding loops; other site 1184267001127 ABC-ATPase subunit interface; other site 1184267001128 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 1184267001129 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 1184267001130 putative PBP binding loops; other site 1184267001131 ABC-ATPase subunit interface; other site 1184267001132 PilZ domain; Region: PilZ; pfam07238 1184267001133 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cl00200 1184267001134 amphipathic channel; other site 1184267001135 Asn-Pro-Ala signature motifs; other site 1184267001136 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cl00200 1184267001137 amphipathic channel; other site 1184267001138 Asn-Pro-Ala signature motifs; other site 1184267001139 isocitrate dehydrogenase; Validated; Region: PRK08299 1184267001140 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 1184267001141 active site 1184267001142 NAD binding site [chemical binding]; other site 1184267001143 metal binding site [ion binding]; metal-binding site 1184267001144 This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats...; Region: EPT_RTPC-like; cl00288 1184267001145 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 1184267001146 putative active site [active] 1184267001147 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 1184267001148 active site 1184267001149 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 1184267001150 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 1184267001151 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 1184267001152 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 1184267001153 Tetramer interface [polypeptide binding]; other site 1184267001154 active site 1184267001155 FMN-binding site [chemical binding]; other site 1184267001156 Predicted membrane protein [Function unknown]; Region: COG2119 1184267001157 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 1184267001158 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 1184267001159 Endonuclease I; Region: Endonuclease_1; pfam04231 1184267001160 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1184267001161 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 1184267001162 S-adenosylmethionine binding site [chemical binding]; other site 1184267001163 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1184267001164 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 1184267001165 chorismate binding enzyme; Region: Chorismate_bind; cl10555 1184267001166 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 1184267001167 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylic-acid synthase; Region: menD; TIGR00173 1184267001168 PYR/PP interface [polypeptide binding]; other site 1184267001169 dimer interface [polypeptide binding]; other site 1184267001170 TPP binding site [chemical binding]; other site 1184267001171 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 1184267001172 TPP-binding site [chemical binding]; other site 1184267001173 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 1184267001174 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 1184267001175 cleavage site 1184267001176 active site 1184267001177 substrate binding sites [chemical binding]; other site 1184267001178 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 1184267001179 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 1184267001180 TAP-like protein; Region: Abhydrolase_4; pfam08386 1184267001181 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 1184267001182 active site 1184267001183 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 1184267001184 TPP-binding site [chemical binding]; other site 1184267001185 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 1184267001186 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 1184267001187 PYR/PP interface [polypeptide binding]; other site 1184267001188 dimer interface [polypeptide binding]; other site 1184267001189 TPP binding site [chemical binding]; other site 1184267001190 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1184267001191 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1184267001192 active site 1184267001193 NTP binding site [chemical binding]; other site 1184267001194 metal binding triad [ion binding]; metal-binding site 1184267001195 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1184267001196 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1184267001197 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1184267001198 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 1184267001199 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 1184267001200 ATP binding site [chemical binding]; other site 1184267001201 Mg++ binding site [ion binding]; other site 1184267001202 motif III; other site 1184267001203 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 1184267001204 nucleotide binding region [chemical binding]; other site 1184267001205 ATP-binding site [chemical binding]; other site 1184267001206 Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only]; Region: SsnA; COG0402 1184267001207 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 1184267001208 active site 1184267001209 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 1184267001210 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 1184267001211 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1184267001212 minor groove reading motif; other site 1184267001213 helix-hairpin-helix signature motif; other site 1184267001214 substrate binding pocket [chemical binding]; other site 1184267001215 active site 1184267001216 Agmatinase-like family includes proclavaminic acid amidinohydrolase; Region: Agmatinase_PAH; cd11592 1184267001217 agmatinase; Region: agmatinase; TIGR01230 1184267001218 oligomer interface [polypeptide binding]; other site 1184267001219 putative active site [active] 1184267001220 Mn binding site [ion binding]; other site 1184267001221 methionine sulfoxide reductase A; Provisional; Region: PRK14054 1184267001222 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267001223 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267001224 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 1184267001225 ABC1 family; Region: ABC1; cl17513 1184267001226 VacB and RNase II family 3'-5' exoribonucleases; Region: 3_prime_RNase; TIGR00358 1184267001227 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 1184267001228 RNB domain; Region: RNB; pfam00773 1184267001229 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 1184267001230 RNA binding site [nucleotide binding]; other site 1184267001231 Outer membrane efflux protein; Region: OEP; pfam02321 1184267001232 Outer membrane efflux protein; Region: OEP; pfam02321 1184267001233 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 1184267001234 Protein export membrane protein; Region: SecD_SecF; cl14618 1184267001235 Zinc dependent phospholipase C/S1-P1 nuclease; Region: ZnPC_S1P1; cl16915 1184267001236 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 1184267001237 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1184267001238 TM-ABC transporter signature motif; other site 1184267001239 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1184267001240 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 1184267001241 TM-ABC transporter signature motif; other site 1184267001242 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 1184267001243 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267001244 Walker A/P-loop; other site 1184267001245 ATP binding site [chemical binding]; other site 1184267001246 Q-loop/lid; other site 1184267001247 ABC transporter signature motif; other site 1184267001248 Walker B; other site 1184267001249 D-loop; other site 1184267001250 H-loop/switch region; other site 1184267001251 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 1184267001252 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 1184267001253 ligand binding site [chemical binding]; other site 1184267001254 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 1184267001255 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1184267001256 PLD-like domain; Region: PLDc_2; pfam13091 1184267001257 putative active site [active] 1184267001258 catalytic site [active] 1184267001259 PLD-like domain; Region: PLDc_2; pfam13091 1184267001260 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1184267001261 putative active site [active] 1184267001262 catalytic site [active] 1184267001263 Domain of unknown function DUF21; Region: DUF21; pfam01595 1184267001264 FOG: CBS domain [General function prediction only]; Region: COG0517 1184267001265 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 1184267001266 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 1184267001267 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1184267001268 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1184267001269 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1184267001270 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 1184267001271 protein binding site [polypeptide binding]; other site 1184267001272 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 1184267001273 Domain interface; other site 1184267001274 Peptide binding site; other site 1184267001275 Active site tetrad [active] 1184267001276 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 1184267001277 homodimer interaction site [polypeptide binding]; other site 1184267001278 cofactor binding site; other site 1184267001279 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 1184267001280 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 1184267001281 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 1184267001282 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267001283 putative catalytic site [active] 1184267001284 putative metal binding site [ion binding]; other site 1184267001285 putative catalytic site [active] 1184267001286 putative phosphate binding site [ion binding]; other site 1184267001287 putative phosphate binding site [ion binding]; other site 1184267001288 putative metal binding site [ion binding]; other site 1184267001289 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 1184267001290 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1184267001291 active site 1184267001292 HIGH motif; other site 1184267001293 nucleotide binding site [chemical binding]; other site 1184267001294 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1184267001295 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 1184267001296 active site 1184267001297 KMSKS motif; other site 1184267001298 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1184267001299 tRNA binding surface [nucleotide binding]; other site 1184267001300 anticodon binding site; other site 1184267001301 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 1184267001302 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 1184267001303 active site residue [active] 1184267001304 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 1184267001305 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1184267001306 putative substrate translocation pore; other site 1184267001307 Uncharacterized ACR, YggU family COG1872; Region: DUF167; pfam02594 1184267001308 DivIVA protein; Region: DivIVA; pfam05103 1184267001309 DivIVA domain; Region: DivI1A_domain; TIGR03544 1184267001310 Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Region: ProC; COG0345 1184267001311 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 1184267001312 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 1184267001313 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1184267001314 catalytic residue [active] 1184267001315 Maf-like protein; Region: Maf; pfam02545 1184267001316 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 1184267001317 active site 1184267001318 dimer interface [polypeptide binding]; other site 1184267001319 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 1184267001320 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1184267001321 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 1184267001322 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 1184267001323 phosphopeptide binding site; other site 1184267001324 PAS domain; Region: PAS_9; pfam13426 1184267001325 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 1184267001326 phosphopeptide binding site; other site 1184267001327 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 1184267001328 TPR motif; other site 1184267001329 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 1184267001330 phosphopeptide binding site; other site 1184267001331 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 1184267001332 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 1184267001333 phosphopeptide binding site; other site 1184267001334 Sulfatase; Region: Sulfatase; cl17466 1184267001335 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 1184267001336 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1184267001337 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 1184267001338 Transposase IS200 like; Region: Y1_Tnp; cl00848 1184267001339 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 1184267001340 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1184267001341 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1184267001342 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1184267001343 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1184267001344 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1184267001345 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1184267001346 dimerization interface 3.5A [polypeptide binding]; other site 1184267001347 active site 1184267001348 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 1184267001349 23S rRNA interface [nucleotide binding]; other site 1184267001350 L3 interface [polypeptide binding]; other site 1184267001351 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1184267001352 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1184267001353 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 1184267001354 non-specific DNA binding site [nucleotide binding]; other site 1184267001355 salt bridge; other site 1184267001356 sequence-specific DNA binding site [nucleotide binding]; other site 1184267001357 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1184267001358 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 1184267001359 ligand binding site [chemical binding]; other site 1184267001360 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 1184267001361 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1184267001362 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 1184267001363 motif 1; other site 1184267001364 active site 1184267001365 motif 2; other site 1184267001366 motif 3; other site 1184267001367 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1184267001368 DHHA1 domain; Region: DHHA1; pfam02272 1184267001369 RecX family; Region: RecX; cl00936 1184267001370 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1184267001371 SPFH domain / Band 7 family; Region: Band_7; pfam01145 1184267001372 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1184267001373 tetramer interfaces [polypeptide binding]; other site 1184267001374 binuclear metal-binding site [ion binding]; other site 1184267001375 Competence-damaged protein; Region: CinA; pfam02464 1184267001376 recombinase A; Provisional; Region: recA; PRK09354 1184267001377 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 1184267001378 hexamer interface [polypeptide binding]; other site 1184267001379 Walker A motif; other site 1184267001380 ATP binding site [chemical binding]; other site 1184267001381 Walker B motif; other site 1184267001382 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 1184267001383 catalytic residues [active] 1184267001384 dimer interface [polypeptide binding]; other site 1184267001385 Aspartokinases [Amino acid transport and metabolism]; Region: LysC; COG0527 1184267001386 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 1184267001387 putative nucleotide binding site [chemical binding]; other site 1184267001388 putative catalytic residues [active] 1184267001389 putative Mg ion binding site [ion binding]; other site 1184267001390 putative aspartate binding site [chemical binding]; other site 1184267001391 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 1184267001392 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1184267001393 catalytic residue [active] 1184267001394 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 1184267001395 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 1184267001396 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 1184267001397 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1184267001398 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1184267001399 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 1184267001400 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 1184267001401 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 1184267001402 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 1184267001403 Rod binding protein; Region: Rod-binding; pfam10135 1184267001404 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 1184267001405 FlgN protein; Region: FlgN; pfam05130 1184267001406 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07739 1184267001407 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1184267001408 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK07701 1184267001409 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1184267001410 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1184267001411 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1184267001412 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1184267001413 putative acyl-acceptor binding pocket; other site 1184267001414 Global regulator protein family; Region: CsrA; pfam02599 1184267001415 FliW protein; Region: FliW; cl00740 1184267001416 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1184267001417 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1184267001418 ATP-binding cassette domain 1 of multidrug resistance-associated protein, subfamily C; Region: ABCC_MRP_domain1; cd03250 1184267001419 Walker A/P-loop; other site 1184267001420 ATP binding site [chemical binding]; other site 1184267001421 Q-loop/lid; other site 1184267001422 ABC transporter signature motif; other site 1184267001423 Walker B; other site 1184267001424 D-loop; other site 1184267001425 H-loop/switch region; other site 1184267001426 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 1184267001427 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1184267001428 ATP-binding cassette domain 2 of multidrug resistance-associated protein; Region: ABCC_MRP_domain2; cd03244 1184267001429 RmuC family; Region: RmuC; pfam02646 1184267001430 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 1184267001431 UbiA prenyltransferase family; Region: UbiA; pfam01040 1184267001432 o-succinylbenzoate synthase; Region: menC_gamma/gm+; TIGR01927 1184267001433 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion; Region: enolase_like; cl17188 1184267001434 metal binding site [ion binding]; metal-binding site 1184267001435 substrate binding pocket [chemical binding]; other site 1184267001436 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 1184267001437 acyl-activating enzyme (AAE) consensus motif; other site 1184267001438 AMP binding site [chemical binding]; other site 1184267001439 active site 1184267001440 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 1184267001441 CoA binding site [chemical binding]; other site 1184267001442 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1184267001443 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1184267001444 Myosin heavy chain [Cytoskeleton]; Region: COG5022 1184267001445 Transglycosylase; Region: Transgly; pfam00912 1184267001446 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 1184267001447 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1184267001448 Protein of unknown function (DUF507); Region: DUF507; cl01112 1184267001449 Protein of unknown function (DUF507); Region: DUF507; cl01112 1184267001450 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 1184267001451 oligomerisation interface [polypeptide binding]; other site 1184267001452 mobile loop; other site 1184267001453 roof hairpin; other site 1184267001454 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 1184267001455 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1184267001456 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1184267001457 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1184267001458 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 1184267001459 RNA binding surface [nucleotide binding]; other site 1184267001460 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 1184267001461 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1184267001462 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 1184267001463 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 1184267001464 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1184267001465 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1184267001466 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1184267001467 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 1184267001468 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 1184267001469 putative active site [active] 1184267001470 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 1184267001471 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 1184267001472 FeS/SAM binding site; other site 1184267001473 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 1184267001474 EamA-like transporter family; Region: EamA; pfam00892 1184267001475 EamA-like transporter family; Region: EamA; pfam00892 1184267001476 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 1184267001477 Part of AAA domain; Region: AAA_19; pfam13245 1184267001478 Family description; Region: UvrD_C_2; pfam13538 1184267001479 Sporulation related domain; Region: SPOR; pfam05036 1184267001480 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1184267001481 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 1184267001482 active site 1184267001483 dimerization interface [polypeptide binding]; other site 1184267001484 FOG: CBS domain [General function prediction only]; Region: COG0517 1184267001485 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 1184267001486 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 1184267001487 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 1184267001488 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 1184267001489 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 1184267001490 flagellar biosynthetic protein FliO; Region: FliO_TIGR; TIGR03500 1184267001491 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 1184267001492 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 1184267001493 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 1184267001494 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 1184267001495 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 1184267001496 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 1184267001497 FHIPEP family; Region: FHIPEP; pfam00771 1184267001498 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 1184267001499 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 1184267001500 septum site-determining protein MinD; Region: minD_bact; TIGR01968 1184267001501 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 1184267001502 P-loop; other site 1184267001503 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 1184267001504 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1184267001505 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1184267001506 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 1184267001507 DNA binding residues [nucleotide binding] 1184267001508 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1184267001509 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1184267001510 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1184267001511 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 1184267001512 DNA binding residues [nucleotide binding] 1184267001513 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; cl09865 1184267001514 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1184267001515 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 1184267001516 dimer interface [polypeptide binding]; other site 1184267001517 anticodon binding site; other site 1184267001518 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 1184267001519 homodimer interface [polypeptide binding]; other site 1184267001520 motif 1; other site 1184267001521 active site 1184267001522 motif 2; other site 1184267001523 GAD domain; Region: GAD; pfam02938 1184267001524 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 1184267001525 active site 1184267001526 motif 3; other site 1184267001527 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 1184267001528 Type II/IV secretion system protein; Region: T2SE; pfam00437 1184267001529 Walker A motif; other site 1184267001530 ATP binding site [chemical binding]; other site 1184267001531 Walker B motif; other site 1184267001532 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1184267001533 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267001534 active site 1184267001535 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267001536 phosphorylation site [posttranslational modification] 1184267001537 intermolecular recognition site; other site 1184267001538 dimerization interface [polypeptide binding]; other site 1184267001539 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 1184267001540 dimer interface [polypeptide binding]; other site 1184267001541 phosphorylation site [posttranslational modification] 1184267001542 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 1184267001543 ATP binding site [chemical binding]; other site 1184267001544 Mg2+ binding site [ion binding]; other site 1184267001545 G-X-G motif; other site 1184267001546 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 1184267001547 active site 1184267001548 Flp/Fap pilin component; Region: Flp_Fap; cl01585 1184267001549 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 1184267001550 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1184267001551 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1184267001552 homodimer interface [polypeptide binding]; other site 1184267001553 NADP binding site [chemical binding]; other site 1184267001554 substrate binding site [chemical binding]; other site 1184267001555 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 1184267001556 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 1184267001557 [2Fe-2S] cluster binding site [ion binding]; other site 1184267001558 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 1184267001559 hydrophobic ligand binding site; other site 1184267001560 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 1184267001561 PUA domain; Region: PUA; cl00607 1184267001562 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 1184267001563 putative RNA binding site [nucleotide binding]; other site 1184267001564 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 1184267001565 S-adenosylmethionine binding site [chemical binding]; other site 1184267001566 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cl02915 1184267001567 pore gating glutamate residue; other site 1184267001568 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 1184267001569 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 1184267001570 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 1184267001571 Cytochrome c; Region: Cytochrom_C; cl11414 1184267001572 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1184267001573 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1184267001574 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 1184267001575 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267001576 active site 1184267001577 phosphorylation site [posttranslational modification] 1184267001578 intermolecular recognition site; other site 1184267001579 dimerization interface [polypeptide binding]; other site 1184267001580 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267001581 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267001582 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 1184267001583 dimer interface [polypeptide binding]; other site 1184267001584 phosphorylation site [posttranslational modification] 1184267001585 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 1184267001586 ATP binding site [chemical binding]; other site 1184267001587 Mg2+ binding site [ion binding]; other site 1184267001588 G-X-G motif; other site 1184267001589 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 1184267001590 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 1184267001591 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 1184267001592 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1184267001593 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1184267001594 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 1184267001595 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 1184267001596 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 1184267001597 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 1184267001598 Ligand Binding Site [chemical binding]; other site 1184267001599 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 1184267001600 GAF domain; Region: GAF_3; pfam13492 1184267001601 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 1184267001602 dimer interface [polypeptide binding]; other site 1184267001603 phosphorylation site [posttranslational modification] 1184267001604 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 1184267001605 ATP binding site [chemical binding]; other site 1184267001606 Mg2+ binding site [ion binding]; other site 1184267001607 G-X-G motif; other site 1184267001608 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 1184267001609 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267001610 active site 1184267001611 phosphorylation site [posttranslational modification] 1184267001612 intermolecular recognition site; other site 1184267001613 dimerization interface [polypeptide binding]; other site 1184267001614 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 1184267001615 DNA binding site [nucleotide binding] 1184267001616 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 1184267001617 lipoyl attachment site [posttranslational modification]; other site 1184267001618 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 1184267001619 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1184267001620 Mitochondrial small ribosomal subunit Rsm22; Region: Rsm22; cl17847 1184267001621 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 1184267001622 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 1184267001623 putative active site [active] 1184267001624 glycine dehydrogenase; Provisional; Region: PRK05367 1184267001625 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 1184267001626 tetramer interface [polypeptide binding]; other site 1184267001627 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267001628 catalytic residue [active] 1184267001629 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 1184267001630 tetramer interface [polypeptide binding]; other site 1184267001631 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267001632 catalytic residue [active] 1184267001633 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 1184267001634 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 1184267001635 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 1184267001636 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 1184267001637 motif 1; other site 1184267001638 dimer interface [polypeptide binding]; other site 1184267001639 active site 1184267001640 motif 2; other site 1184267001641 motif 3; other site 1184267001642 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 1184267001643 active site 1184267001644 substrate binding sites [chemical binding]; other site 1184267001645 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 1184267001646 IHF - DNA interface [nucleotide binding]; other site 1184267001647 IHF dimer interface [polypeptide binding]; other site 1184267001648 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 1184267001649 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1184267001650 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 1184267001651 active site 1184267001652 8-oxo-dGMP binding site [chemical binding]; other site 1184267001653 nudix motif; other site 1184267001654 metal binding site [ion binding]; metal-binding site 1184267001655 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 1184267001656 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 1184267001657 quinone interaction residues [chemical binding]; other site 1184267001658 active site 1184267001659 catalytic residues [active] 1184267001660 FMN binding site [chemical binding]; other site 1184267001661 substrate binding site [chemical binding]; other site 1184267001662 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 1184267001663 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 1184267001664 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 1184267001665 NAD(P) binding site [chemical binding]; other site 1184267001666 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; pfam13532 1184267001667 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 1184267001668 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1184267001669 putative ribose interaction site [chemical binding]; other site 1184267001670 putative ADP binding site [chemical binding]; other site 1184267001671 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 1184267001672 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 1184267001673 FeS/SAM binding site; other site 1184267001674 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 1184267001675 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 1184267001676 substrate binding site [chemical binding]; other site 1184267001677 ATP binding site [chemical binding]; other site 1184267001678 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 1184267001679 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 1184267001680 putative active site [active] 1184267001681 putative metal binding site [ion binding]; other site 1184267001682 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 1184267001683 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 1184267001684 phosphopeptide binding site; other site 1184267001685 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1184267001686 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1184267001687 metal binding site [ion binding]; metal-binding site 1184267001688 active site 1184267001689 I-site; other site 1184267001690 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 1184267001691 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1184267001692 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 1184267001693 DNA binding residues [nucleotide binding] 1184267001694 Predicted aminopeptidase (DUF2265); Region: DUF2265; cl17720 1184267001695 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 1184267001696 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; cl03075 1184267001697 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 1184267001698 PilZ domain; Region: PilZ; pfam07238 1184267001699 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 1184267001700 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 1184267001701 putative active site [active] 1184267001702 PhoH-like protein; Region: PhoH; pfam02562 1184267001703 (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 1184267001704 dimer interaction site [polypeptide binding]; other site 1184267001705 substrate-binding tunnel; other site 1184267001706 active site 1184267001707 catalytic site [active] 1184267001708 substrate binding site [chemical binding]; other site 1184267001709 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267001710 putative active site [active] 1184267001711 heme pocket [chemical binding]; other site 1184267001712 PAS domain S-box; Region: sensory_box; TIGR00229 1184267001713 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267001714 putative active site [active] 1184267001715 heme pocket [chemical binding]; other site 1184267001716 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267001717 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 1184267001718 dimer interface [polypeptide binding]; other site 1184267001719 phosphorylation site [posttranslational modification] 1184267001720 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 1184267001721 ATP binding site [chemical binding]; other site 1184267001722 G-X-G motif; other site 1184267001723 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1184267001724 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1184267001725 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1184267001726 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1184267001727 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1184267001728 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 1184267001729 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 1184267001730 E3 interaction surface; other site 1184267001731 lipoyl attachment site [posttranslational modification]; other site 1184267001732 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 1184267001733 E3 interaction surface; other site 1184267001734 lipoyl attachment site [posttranslational modification]; other site 1184267001735 e3 binding domain; Region: E3_binding; pfam02817 1184267001736 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1184267001737 lipoyl synthase; Provisional; Region: PRK05481 1184267001738 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 1184267001739 FeS/SAM binding site; other site 1184267001740 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1184267001741 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1184267001742 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1184267001743 active site 1184267001744 HIGH motif; other site 1184267001745 KMSK motif region; other site 1184267001746 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1184267001747 tRNA binding surface [nucleotide binding]; other site 1184267001748 anticodon binding site; other site 1184267001749 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1184267001750 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267001751 active site 1184267001752 phosphorylation site [posttranslational modification] 1184267001753 intermolecular recognition site; other site 1184267001754 dimerization interface [polypeptide binding]; other site 1184267001755 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 1184267001756 DNA binding site [nucleotide binding] 1184267001757 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 1184267001758 dimerization interface [polypeptide binding]; other site 1184267001759 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267001760 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 1184267001761 dimer interface [polypeptide binding]; other site 1184267001762 phosphorylation site [posttranslational modification] 1184267001763 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 1184267001764 ATP binding site [chemical binding]; other site 1184267001765 Mg2+ binding site [ion binding]; other site 1184267001766 G-X-G motif; other site 1184267001767 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 1184267001768 Thioredoxin; Region: Thioredoxin_4; pfam13462 1184267001769 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1184267001770 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 1184267001771 Type II/IV secretion system protein; Region: T2SE; pfam00437 1184267001772 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 1184267001773 ATP binding site [chemical binding]; other site 1184267001774 Walker A motif; other site 1184267001775 hexamer interface [polypeptide binding]; other site 1184267001776 Walker B motif; other site 1184267001777 enolase; Provisional; Region: eno; PRK00077 1184267001778 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 1184267001779 dimer interface [polypeptide binding]; other site 1184267001780 metal binding site [ion binding]; metal-binding site 1184267001781 substrate binding pocket [chemical binding]; other site 1184267001782 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1184267001783 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1184267001784 ligand binding site [chemical binding]; other site 1184267001785 Septum formation initiator; Region: DivIC; cl17659 1184267001786 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1184267001787 DNA polymerase I; Region: pola; TIGR00593 1184267001788 active site 1184267001789 metal binding site 1 [ion binding]; metal-binding site 1184267001790 putative 5' ssDNA interaction site; other site 1184267001791 metal binding site 3; metal-binding site 1184267001792 metal binding site 2 [ion binding]; metal-binding site 1184267001793 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1184267001794 putative DNA binding site [nucleotide binding]; other site 1184267001795 putative metal binding site [ion binding]; other site 1184267001796 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1184267001797 active site 1184267001798 substrate binding site [chemical binding]; other site 1184267001799 catalytic site [active] 1184267001800 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1184267001801 active site 1184267001802 DNA binding site [nucleotide binding] 1184267001803 catalytic site [active] 1184267001804 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 1184267001805 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 1184267001806 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 1184267001807 phosphopeptide binding site; other site 1184267001808 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 1184267001809 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 1184267001810 Walker A motif; other site 1184267001811 ATP binding site [chemical binding]; other site 1184267001812 Walker B motif; other site 1184267001813 arginine finger; other site 1184267001814 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267001815 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1184267001816 G1 box; other site 1184267001817 GTP/Mg2+ binding site [chemical binding]; other site 1184267001818 Switch I region; other site 1184267001819 G2 box; other site 1184267001820 G3 box; other site 1184267001821 Switch II region; other site 1184267001822 G4 box; other site 1184267001823 G5 box; other site 1184267001824 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1184267001825 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1184267001826 Ligand binding site; other site 1184267001827 oligomer interface; other site 1184267001828 CTP synthetase; Validated; Region: pyrG; PRK05380 1184267001829 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 1184267001830 Catalytic site [active] 1184267001831 active site 1184267001832 UTP binding site [chemical binding]; other site 1184267001833 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1184267001834 active site 1184267001835 putative oxyanion hole; other site 1184267001836 catalytic triad [active] 1184267001837 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 1184267001838 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 1184267001839 putative active site [active] 1184267001840 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 1184267001841 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 1184267001842 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 1184267001843 active site 1184267001844 motif I; other site 1184267001845 motif II; other site 1184267001846 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1184267001847 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 1184267001848 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 1184267001849 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 1184267001850 binding surface 1184267001851 TPR repeat; Region: TPR_11; pfam13414 1184267001852 TPR motif; other site 1184267001853 TPR repeat; Region: TPR_11; pfam13414 1184267001854 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 1184267001855 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 1184267001856 phosphopeptide binding site; other site 1184267001857 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 1184267001858 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1184267001859 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 1184267001860 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1184267001861 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 1184267001862 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 1184267001863 OstA-like protein; Region: OstA; cl00844 1184267001864 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1184267001865 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 1184267001866 Walker A/P-loop; other site 1184267001867 ATP binding site [chemical binding]; other site 1184267001868 Q-loop/lid; other site 1184267001869 ABC transporter signature motif; other site 1184267001870 Walker B; other site 1184267001871 D-loop; other site 1184267001872 H-loop/switch region; other site 1184267001873 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 1184267001874 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 1184267001875 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 1184267001876 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 1184267001877 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1184267001878 active site 1184267001879 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 1184267001880 30S subunit binding site; other site 1184267001881 S-adenosylmethionine synthetase; Validated; Region: PRK05250 1184267001882 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 1184267001883 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1184267001884 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1184267001885 GTP-binding protein LepA; Provisional; Region: PRK05433 1184267001886 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1184267001887 G1 box; other site 1184267001888 putative GEF interaction site [polypeptide binding]; other site 1184267001889 GTP/Mg2+ binding site [chemical binding]; other site 1184267001890 Switch I region; other site 1184267001891 G2 box; other site 1184267001892 G3 box; other site 1184267001893 Switch II region; other site 1184267001894 G4 box; other site 1184267001895 G5 box; other site 1184267001896 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 1184267001897 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 1184267001898 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1184267001899 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1184267001900 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 1184267001901 Catalytic site [active] 1184267001902 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 1184267001903 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1184267001904 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 1184267001905 Catalytic site [active] 1184267001906 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 1184267001907 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1184267001908 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 1184267001909 Catalytic site [active] 1184267001910 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 1184267001911 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 1184267001912 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 1184267001913 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 1184267001914 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 1184267001915 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 1184267001916 catalytic site [active] 1184267001917 subunit interface [polypeptide binding]; other site 1184267001918 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 1184267001919 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1184267001920 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1184267001921 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 1184267001922 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1184267001923 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1184267001924 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 1184267001925 IMP binding site; other site 1184267001926 dimer interface [polypeptide binding]; other site 1184267001927 interdomain contacts; other site 1184267001928 partial ornithine binding site; other site 1184267001929 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 1184267001930 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 1184267001931 substrate binding pocket [chemical binding]; other site 1184267001932 membrane-bound complex binding site; other site 1184267001933 hinge residues; other site 1184267001934 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 1184267001935 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267001936 Walker A/P-loop; other site 1184267001937 ATP binding site [chemical binding]; other site 1184267001938 Q-loop/lid; other site 1184267001939 ABC transporter signature motif; other site 1184267001940 Walker B; other site 1184267001941 D-loop; other site 1184267001942 H-loop/switch region; other site 1184267001943 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 1184267001944 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 1184267001945 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 1184267001946 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 1184267001947 Competence protein A; Region: Competence_A; pfam11104 1184267001948 Cell division protein FtsA; Region: FtsA; cl17206 1184267001949 Cell division protein FtsA; Region: FtsA; pfam14450 1184267001950 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 1184267001951 Pilus assembly protein, PilO; Region: PilO; cl01234 1184267001952 Pilus assembly protein, PilP; Region: PilP; pfam04351 1184267001953 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 1184267001954 Secretin and TonB N terminus short domain; Region: STN; smart00965 1184267001955 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1184267001956 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1184267001957 Cupin domain; Region: Cupin_2; pfam07883 1184267001958 Flagellar motor switch protein [Cell motility and secretion]; Region: FliG; COG1536 1184267001959 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 1184267001960 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 1184267001961 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 1184267001962 putative ion selectivity filter; other site 1184267001963 putative pore gating glutamate residue; other site 1184267001964 putative H+/Cl- coupling transport residue; other site 1184267001965 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1184267001966 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 1184267001967 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1184267001968 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1184267001969 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 1184267001970 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 1184267001971 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1184267001972 RNA binding site [nucleotide binding]; other site 1184267001973 nitrilase; Region: PLN02798 1184267001974 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 1184267001975 putative active site [active] 1184267001976 catalytic triad [active] 1184267001977 dimer interface [polypeptide binding]; other site 1184267001978 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 1184267001979 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1184267001980 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 1184267001981 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 1184267001982 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 1184267001983 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 1184267001984 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1184267001985 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 1184267001986 trimer interface [polypeptide binding]; other site 1184267001987 active site 1184267001988 UDP-GlcNAc binding site [chemical binding]; other site 1184267001989 lipid binding site [chemical binding]; lipid-binding site 1184267001990 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 1184267001991 rRNA binding site [nucleotide binding]; other site 1184267001992 predicted 30S ribosome binding site; other site 1184267001993 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 1184267001994 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 1184267001995 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 1184267001996 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 1184267001997 RNA binding site [nucleotide binding]; other site 1184267001998 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 1184267001999 catalytic core [active] 1184267002000 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 1184267002001 Ubiquitin-activating enzyme e1 C-terminal domain; Region: UBA_e1_C; cl09615 1184267002002 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 1184267002003 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 1184267002004 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 1184267002005 active site 1184267002006 interdomain interaction site; other site 1184267002007 putative metal-binding site [ion binding]; other site 1184267002008 nucleotide binding site [chemical binding]; other site 1184267002009 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 1184267002010 domain I; other site 1184267002011 DNA binding groove [nucleotide binding] 1184267002012 phosphate binding site [ion binding]; other site 1184267002013 domain II; other site 1184267002014 domain III; other site 1184267002015 nucleotide binding site [chemical binding]; other site 1184267002016 catalytic site [active] 1184267002017 domain IV; other site 1184267002018 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1184267002019 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1184267002020 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1184267002021 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1184267002022 C-terminal peptidase (prc); Region: prc; TIGR00225 1184267002023 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 1184267002024 protein binding site [polypeptide binding]; other site 1184267002025 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1184267002026 Catalytic dyad [active] 1184267002027 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 1184267002028 heat shock protein HtpX; Provisional; Region: PRK05457 1184267002029 heat shock protein HtpX; Provisional; Region: PRK05457 1184267002030 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1184267002031 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 1184267002032 tetramer interface [polypeptide binding]; other site 1184267002033 TPP-binding site [chemical binding]; other site 1184267002034 heterodimer interface [polypeptide binding]; other site 1184267002035 phosphorylation loop region [posttranslational modification] 1184267002036 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 1184267002037 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 1184267002038 PYR/PP interface [polypeptide binding]; other site 1184267002039 dimer interface [polypeptide binding]; other site 1184267002040 TPP binding site [chemical binding]; other site 1184267002041 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1184267002042 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 1184267002043 S-adenosylmethionine binding site [chemical binding]; other site 1184267002044 Dihydroneopterin aldolase; Region: FolB; smart00905 1184267002045 active site 1184267002046 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 1184267002047 catalytic center binding site [active] 1184267002048 ATP binding site [chemical binding]; other site 1184267002049 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 1184267002050 dihydropteroate synthase; Region: DHPS; TIGR01496 1184267002051 substrate binding pocket [chemical binding]; other site 1184267002052 dimer interface [polypeptide binding]; other site 1184267002053 inhibitor binding site; inhibition site 1184267002054 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1184267002055 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1184267002056 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 1184267002057 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1184267002058 putative active site [active] 1184267002059 putative metal binding site [ion binding]; other site 1184267002060 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1184267002061 active site 1184267002062 Domain of unknown function DUF21; Region: DUF21; pfam01595 1184267002063 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 1184267002064 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1184267002065 elongation factor G; Reviewed; Region: PRK12740 1184267002066 G1 box; other site 1184267002067 putative GEF interaction site [polypeptide binding]; other site 1184267002068 GTP/Mg2+ binding site [chemical binding]; other site 1184267002069 Switch I region; other site 1184267002070 G2 box; other site 1184267002071 G3 box; other site 1184267002072 Switch II region; other site 1184267002073 G4 box; other site 1184267002074 G5 box; other site 1184267002075 mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating...; Region: mtEFG1_II_like; cd04091 1184267002076 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 1184267002077 mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating...; Region: mtEFG1_C; cd04097 1184267002078 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1184267002079 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 1184267002080 ATP binding site [chemical binding]; other site 1184267002081 putative Mg++ binding site [ion binding]; other site 1184267002082 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 1184267002083 nucleotide binding region [chemical binding]; other site 1184267002084 ATP-binding site [chemical binding]; other site 1184267002085 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 1184267002086 PilZ domain; Region: PilZ; pfam07238 1184267002087 polyphosphate kinase; Provisional; Region: PRK05443 1184267002088 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 1184267002089 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 1184267002090 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 1184267002091 putative domain interface [polypeptide binding]; other site 1184267002092 putative active site [active] 1184267002093 catalytic site [active] 1184267002094 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1184267002095 putative active site [active] 1184267002096 catalytic site [active] 1184267002097 exopolyphosphatase; Region: exo_poly_only; TIGR03706 1184267002098 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1184267002099 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 1184267002100 PhoU domain; Region: PhoU; pfam01895 1184267002101 PhoU domain; Region: PhoU; pfam01895 1184267002102 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1184267002103 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267002104 active site 1184267002105 phosphorylation site [posttranslational modification] 1184267002106 intermolecular recognition site; other site 1184267002107 dimerization interface [polypeptide binding]; other site 1184267002108 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 1184267002109 DNA binding site [nucleotide binding] 1184267002110 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267002111 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 1184267002112 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 1184267002113 dimer interface [polypeptide binding]; other site 1184267002114 phosphorylation site [posttranslational modification] 1184267002115 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 1184267002116 ATP binding site [chemical binding]; other site 1184267002117 Mg2+ binding site [ion binding]; other site 1184267002118 G-X-G motif; other site 1184267002119 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 1184267002120 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 1184267002121 S-adenosylmethionine binding site [chemical binding]; other site 1184267002122 Domain of unknown function (DUF814); Region: DUF814; pfam05670 1184267002123 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 1184267002124 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1184267002125 Walker A/P-loop; other site 1184267002126 ATP binding site [chemical binding]; other site 1184267002127 Q-loop/lid; other site 1184267002128 ABC transporter signature motif; other site 1184267002129 Walker B; other site 1184267002130 D-loop; other site 1184267002131 H-loop/switch region; other site 1184267002132 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 1184267002133 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 1184267002134 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 1184267002135 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 1184267002136 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 1184267002137 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]; Region: COG2605 1184267002138 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 1184267002139 Uncharacterized conserved protein (DUF2183); Region: DUF2183; pfam09949 1184267002140 Preprotein translocase SecG subunit; Region: SecG; pfam03840 1184267002141 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 1184267002142 thymidylate kinase; Validated; Region: tmk; PRK00698 1184267002143 TMP-binding site; other site 1184267002144 ATP-binding site [chemical binding]; other site 1184267002145 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 1184267002146 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 1184267002147 Walker A motif; other site 1184267002148 ATP binding site [chemical binding]; other site 1184267002149 Walker B motif; other site 1184267002150 arginine finger; other site 1184267002151 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1184267002152 active site 1184267002153 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 1184267002154 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 1184267002155 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1184267002156 Phosphoglycerate kinase; Region: PGK; pfam00162 1184267002157 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 1184267002158 substrate binding site [chemical binding]; other site 1184267002159 hinge regions; other site 1184267002160 ADP binding site [chemical binding]; other site 1184267002161 catalytic site [active] 1184267002162 triosephosphate isomerase; Provisional; Region: PRK14567 1184267002163 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 1184267002164 substrate binding site [chemical binding]; other site 1184267002165 dimer interface [polypeptide binding]; other site 1184267002166 catalytic triad [active] 1184267002167 threonine dehydratase; Provisional; Region: PRK08198 1184267002168 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 1184267002169 tetramer interface [polypeptide binding]; other site 1184267002170 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267002171 catalytic residue [active] 1184267002172 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 1184267002173 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 1184267002174 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 1184267002175 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267002176 homodimer interface [polypeptide binding]; other site 1184267002177 catalytic residue [active] 1184267002178 cytidylate kinase; Provisional; Region: cmk; PRK00023 1184267002179 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 1184267002180 CMP-binding site; other site 1184267002181 The sites determining sugar specificity; other site 1184267002182 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1184267002183 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 1184267002184 RNA binding site [nucleotide binding]; other site 1184267002185 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 1184267002186 RNA binding site [nucleotide binding]; other site 1184267002187 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 1184267002188 RNA binding site [nucleotide binding]; other site 1184267002189 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 1184267002190 RNA binding site [nucleotide binding]; other site 1184267002191 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 1184267002192 RNA binding site [nucleotide binding]; other site 1184267002193 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 1184267002194 RNA binding site [nucleotide binding]; other site 1184267002195 domain interface; other site 1184267002196 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1184267002197 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1184267002198 tandem repeat interface [polypeptide binding]; other site 1184267002199 oligomer interface [polypeptide binding]; other site 1184267002200 active site residues [active] 1184267002201 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 1184267002202 nucleotide binding site/active site [active] 1184267002203 HIT family signature motif; other site 1184267002204 catalytic residue [active] 1184267002205 Rhomboid family; Region: Rhomboid; pfam01694 1184267002206 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 1184267002207 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 1184267002208 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK07718 1184267002209 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 1184267002210 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267002211 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267002212 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 1184267002213 dimerization interface [polypeptide binding]; other site 1184267002214 Kinase/pyrophosphorylase; Region: Kinase-PPPase; pfam03618 1184267002215 transcription antitermination factor NusB; Region: nusB; TIGR01951 1184267002216 putative RNA binding site [nucleotide binding]; other site 1184267002217 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 1184267002218 ATP cone domain; Region: ATP-cone; pfam03477 1184267002219 16S rRNA methyltransferase B; Provisional; Region: PRK14902 1184267002220 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 1184267002221 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 1184267002222 S-adenosylmethionine binding site [chemical binding]; other site 1184267002223 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 1184267002224 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 1184267002225 substrate binding site [chemical binding]; other site 1184267002226 oxyanion hole (OAH) forming residues; other site 1184267002227 trimer interface [polypeptide binding]; other site 1184267002228 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1184267002229 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1184267002230 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 1184267002231 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1184267002232 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1184267002233 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 1184267002234 dimer interface [polypeptide binding]; other site 1184267002235 motif 1; other site 1184267002236 active site 1184267002237 motif 2; other site 1184267002238 motif 3; other site 1184267002239 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 1184267002240 anticodon binding site; other site 1184267002241 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 1184267002242 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1184267002243 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1184267002244 Walker A/P-loop; other site 1184267002245 ATP binding site [chemical binding]; other site 1184267002246 Q-loop/lid; other site 1184267002247 ABC transporter signature motif; other site 1184267002248 Walker B; other site 1184267002249 D-loop; other site 1184267002250 H-loop/switch region; other site 1184267002251 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1184267002252 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 1184267002253 FtsX-like permease family; Region: FtsX; pfam02687 1184267002254 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 1184267002255 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1184267002256 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1184267002257 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1184267002258 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 1184267002259 ATP binding site [chemical binding]; other site 1184267002260 Mg++ binding site [ion binding]; other site 1184267002261 motif III; other site 1184267002262 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 1184267002263 nucleotide binding region [chemical binding]; other site 1184267002264 ATP-binding site [chemical binding]; other site 1184267002265 Class II Aldolase and Adducin N-terminal domain; Region: Aldolase_II; pfam00596 1184267002266 intersubunit interface [polypeptide binding]; other site 1184267002267 active site 1184267002268 Zn2+ binding site [ion binding]; other site 1184267002269 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 1184267002270 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 1184267002271 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 1184267002272 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1184267002273 The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold; Region: PBP2_thermophilic_Hb8_like; cd08513 1184267002274 peptide binding site [polypeptide binding]; other site 1184267002275 dimer interface [polypeptide binding]; other site 1184267002276 Cytochrome C biogenesis protein; Region: CcmH; cl01179 1184267002277 regulatory protein SpoVG; Reviewed; Region: PRK13259 1184267002278 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 1184267002279 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 1184267002280 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 1184267002281 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 1184267002282 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 1184267002283 Propeptide_C25; Region: Propeptide_C25; pfam08126 1184267002284 Peptidase C25 family N-terminal domain, found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and related proteins; Region: Peptidase_C25_N; cl03181 1184267002285 active site 1184267002286 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1184267002287 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 1184267002288 protein binding site [polypeptide binding]; other site 1184267002289 Domain of unknown function (DUF1844); Region: DUF1844; pfam08899 1184267002290 MoxR-like ATPases [General function prediction only]; Region: COG0714 1184267002291 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 1184267002292 Walker A motif; other site 1184267002293 ATP binding site [chemical binding]; other site 1184267002294 Walker B motif; other site 1184267002295 arginine finger; other site 1184267002296 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 1184267002297 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 1184267002298 metal ion-dependent adhesion site (MIDAS); other site 1184267002299 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 1184267002300 metal ion-dependent adhesion site (MIDAS); other site 1184267002301 von Willebrand factor type A domain; Region: VWA_2; pfam13519 1184267002302 metal ion-dependent adhesion site (MIDAS); other site 1184267002303 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 1184267002304 TPR motif; other site 1184267002305 binding surface 1184267002306 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1184267002307 Oxygen tolerance; Region: BatD; pfam13584 1184267002308 Oxygen tolerance; Region: BatD; pfam13584 1184267002309 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 1184267002310 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 1184267002311 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1184267002312 catalytic residue [active] 1184267002313 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1184267002314 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1184267002315 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1184267002316 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267002317 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267002318 ABC transporter; Region: ABC_tran_2; pfam12848 1184267002319 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267002320 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1184267002321 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 1184267002322 glycyl-tRNA synthetase; Provisional; Region: PRK04173 1184267002323 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 1184267002324 dimer interface [polypeptide binding]; other site 1184267002325 motif 1; other site 1184267002326 active site 1184267002327 motif 2; other site 1184267002328 motif 3; other site 1184267002329 GlyRS Glycyl-anticodon binding domain. GlyRS 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: GlyRS_anticodon; cd00858 1184267002330 anticodon binding site; other site 1184267002331 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1184267002332 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1184267002333 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1184267002334 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1184267002335 cyclase homology domain; Region: CHD; cd07302 1184267002336 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 1184267002337 nucleotidyl binding site; other site 1184267002338 metal binding site [ion binding]; metal-binding site 1184267002339 dimer interface [polypeptide binding]; other site 1184267002340 PilZ domain; Region: PilZ; pfam07238 1184267002341 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1184267002342 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1184267002343 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1184267002344 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 1184267002345 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 1184267002346 putative active site [active] 1184267002347 metal binding site [ion binding]; metal-binding site 1184267002348 YceI-like domain; Region: YceI; smart00867 1184267002349 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267002350 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267002351 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 1184267002352 putative effector binding pocket; other site 1184267002353 dimerization interface [polypeptide binding]; other site 1184267002354 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 1184267002355 PilZ domain; Region: PilZ; pfam07238 1184267002356 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 1184267002357 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 1184267002358 homodimer interface [polypeptide binding]; other site 1184267002359 metal binding site [ion binding]; metal-binding site 1184267002360 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 1184267002361 homodimer interface [polypeptide binding]; other site 1184267002362 active site 1184267002363 putative chemical substrate binding site [chemical binding]; other site 1184267002364 metal binding site [ion binding]; metal-binding site 1184267002365 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 1184267002366 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267002367 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 1184267002368 ATP binding site [chemical binding]; other site 1184267002369 Mg2+ binding site [ion binding]; other site 1184267002370 G-X-G motif; other site 1184267002371 YcaO-like family; Region: YcaO; pfam02624 1184267002372 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 1184267002373 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cl11442 1184267002374 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 1184267002375 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 1184267002376 CRISPR-associated protein Cas9/Csn1, subtype II/NMEMI; Region: cas_Csn1; TIGR01865 1184267002377 peptide chain release factor 2; Provisional; Region: PRK05589 1184267002378 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1184267002379 RF-1 domain; Region: RF-1; pfam00472 1184267002380 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 1184267002381 FtsX-like permease family; Region: FtsX; pfam02687 1184267002382 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1184267002383 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1184267002384 Walker A/P-loop; other site 1184267002385 ATP binding site [chemical binding]; other site 1184267002386 Q-loop/lid; other site 1184267002387 ABC transporter signature motif; other site 1184267002388 Walker B; other site 1184267002389 D-loop; other site 1184267002390 H-loop/switch region; other site 1184267002391 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 1184267002392 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1184267002393 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1184267002394 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1184267002395 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1184267002396 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1184267002397 Surface antigen; Region: Bac_surface_Ag; pfam01103 1184267002398 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 1184267002399 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 1184267002400 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 1184267002401 active site 1184267002402 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1184267002403 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1184267002404 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1184267002405 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1184267002406 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1184267002407 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 1184267002408 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1184267002409 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1184267002410 putative acyl-acceptor binding pocket; other site 1184267002411 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 1184267002412 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1184267002413 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 1184267002414 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 1184267002415 putative active site [active] 1184267002416 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1184267002417 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267002418 active site 1184267002419 phosphorylation site [posttranslational modification] 1184267002420 intermolecular recognition site; other site 1184267002421 dimerization interface [polypeptide binding]; other site 1184267002422 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 1184267002423 Walker A motif; other site 1184267002424 ATP binding site [chemical binding]; other site 1184267002425 Walker B motif; other site 1184267002426 arginine finger; other site 1184267002427 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 1184267002428 CHASE2 domain; Region: CHASE2; pfam05226 1184267002429 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 1184267002430 dimer interface [polypeptide binding]; other site 1184267002431 phosphorylation site [posttranslational modification] 1184267002432 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 1184267002433 ATP binding site [chemical binding]; other site 1184267002434 Mg2+ binding site [ion binding]; other site 1184267002435 G-X-G motif; other site 1184267002436 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 1184267002437 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 1184267002438 active site 1184267002439 Riboflavin kinase; Region: Flavokinase; pfam01687 1184267002440 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 1184267002441 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 1184267002442 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 1184267002443 Walker A motif; other site 1184267002444 ATP binding site [chemical binding]; other site 1184267002445 Walker B motif; other site 1184267002446 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 1184267002447 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 1184267002448 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1184267002449 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1184267002450 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 1184267002451 phosphorylation site [posttranslational modification] 1184267002452 dimer interface [polypeptide binding]; other site 1184267002453 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 1184267002454 ATP binding site [chemical binding]; other site 1184267002455 Mg2+ binding site [ion binding]; other site 1184267002456 G-X-G motif; other site 1184267002457 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1184267002458 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267002459 active site 1184267002460 phosphorylation site [posttranslational modification] 1184267002461 intermolecular recognition site; other site 1184267002462 dimerization interface [polypeptide binding]; other site 1184267002463 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 1184267002464 Walker A motif; other site 1184267002465 ATP binding site [chemical binding]; other site 1184267002466 Walker B motif; other site 1184267002467 arginine finger; other site 1184267002468 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 1184267002469 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267002470 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 1184267002471 dimerization interface [polypeptide binding]; other site 1184267002472 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 1184267002473 dimer interface [polypeptide binding]; other site 1184267002474 phosphorylation site [posttranslational modification] 1184267002475 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 1184267002476 ATP binding site [chemical binding]; other site 1184267002477 Mg2+ binding site [ion binding]; other site 1184267002478 G-X-G motif; other site 1184267002479 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1184267002480 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267002481 active site 1184267002482 phosphorylation site [posttranslational modification] 1184267002483 intermolecular recognition site; other site 1184267002484 dimerization interface [polypeptide binding]; other site 1184267002485 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 1184267002486 DNA binding site [nucleotide binding] 1184267002487 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1184267002488 EamA-like transporter family; Region: EamA; pfam00892 1184267002489 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 1184267002490 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 1184267002491 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1184267002492 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 1184267002493 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 1184267002494 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 1184267002495 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 1184267002496 putative substrate binding pocket [chemical binding]; other site 1184267002497 AC domain interface; other site 1184267002498 catalytic triad [active] 1184267002499 AB domain interface; other site 1184267002500 interchain disulfide; other site 1184267002501 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 1184267002502 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267002503 putative catalytic site [active] 1184267002504 putative metal binding site [ion binding]; other site 1184267002505 putative phosphate binding site [ion binding]; other site 1184267002506 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 1184267002507 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 1184267002508 interface (dimer of trimers) [polypeptide binding]; other site 1184267002509 Substrate-binding/catalytic site; other site 1184267002510 Zn-binding sites [ion binding]; other site 1184267002511 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1184267002512 active site 1184267002513 HIGH motif; other site 1184267002514 nucleotide binding site [chemical binding]; other site 1184267002515 Protein of unknown function (DUF502); Region: DUF502; cl01107 1184267002516 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 1184267002517 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1184267002518 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1184267002519 ligand binding site [chemical binding]; other site 1184267002520 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 1184267002521 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267002522 catalytic triad [active] 1184267002523 putative active site [active] 1184267002524 PilZ domain; Region: PilZ; pfam07238 1184267002525 MgtE intracellular N domain; Region: MgtE_N; pfam03448 1184267002526 Mg2+ transporter (mgtE); Region: mgtE; TIGR00400 1184267002527 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 1184267002528 Divalent cation transporter; Region: MgtE; pfam01769 1184267002529 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1184267002530 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1184267002531 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267002532 Walker A/P-loop; other site 1184267002533 ATP binding site [chemical binding]; other site 1184267002534 Q-loop/lid; other site 1184267002535 ABC transporter signature motif; other site 1184267002536 Walker B; other site 1184267002537 D-loop; other site 1184267002538 H-loop/switch region; other site 1184267002539 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1184267002540 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 1184267002541 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267002542 Walker A/P-loop; other site 1184267002543 ATP binding site [chemical binding]; other site 1184267002544 Q-loop/lid; other site 1184267002545 ABC transporter signature motif; other site 1184267002546 Walker B; other site 1184267002547 D-loop; other site 1184267002548 H-loop/switch region; other site 1184267002549 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1184267002550 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 1184267002551 GTP cyclohydrolase I; Provisional; Region: PLN03044 1184267002552 active site 1184267002553 aminopeptidase N; Provisional; Region: pepN; PRK14015 1184267002554 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 1184267002555 active site 1184267002556 Zn binding site [ion binding]; other site 1184267002557 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 1184267002558 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 1184267002559 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1184267002560 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 1184267002561 dimer interface [polypeptide binding]; other site 1184267002562 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1184267002563 catalytic triad [active] 1184267002564 peroxidatic and resolving cysteines [active] 1184267002565 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 1184267002566 metal ion transporter CorA-like divalent cation transporter superfamily; Region: MIT_CorA-like; cl00459 1184267002567 oligomer interface [polypeptide binding]; other site 1184267002568 citrate synthase; Provisional; Region: PRK14033 1184267002569 Cold-active citrate synthase (CS) from an Antarctic bacterial strain DS2-3R (Ds)-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...; Region: DsCS_like; cd06111 1184267002570 dimer interface [polypeptide binding]; other site 1184267002571 active site 1184267002572 citrylCoA binding site [chemical binding]; other site 1184267002573 oxalacetate/citrate binding site [chemical binding]; other site 1184267002574 coenzyme A binding site [chemical binding]; other site 1184267002575 catalytic triad [active] 1184267002576 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 1184267002577 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 1184267002578 tetramer interface [polypeptide binding]; other site 1184267002579 active site 1184267002580 Mg2+/Mn2+ binding site [ion binding]; other site 1184267002581 Uncharacterized protein involved in propionate catabolism [General function prediction only]; Region: PrpD; COG2079 1184267002582 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1184267002583 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1184267002584 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1184267002585 Surface antigen; Region: Bac_surface_Ag; pfam01103 1184267002586 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1184267002587 Family of unknown function (DUF490); Region: DUF490; pfam04357 1184267002588 elongation factor P; Validated; Region: PRK00529 1184267002589 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1184267002590 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 1184267002591 RNA binding site [nucleotide binding]; other site 1184267002592 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 1184267002593 RNA binding site [nucleotide binding]; other site 1184267002594 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 1184267002595 TPR motif; other site 1184267002596 binding surface 1184267002597 TPR repeat; Region: TPR_11; pfam13414 1184267002598 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 1184267002599 active site 1184267002600 putative DNA-binding cleft [nucleotide binding]; other site 1184267002601 dimer interface [polypeptide binding]; other site 1184267002602 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1184267002603 RuvA N terminal domain; Region: RuvA_N; pfam01330 1184267002604 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1184267002605 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1184267002606 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 1184267002607 Walker A motif; other site 1184267002608 ATP binding site [chemical binding]; other site 1184267002609 Walker B motif; other site 1184267002610 arginine finger; other site 1184267002611 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1184267002612 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1184267002613 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1184267002614 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 1184267002615 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 1184267002616 hexamer interface [polypeptide binding]; other site 1184267002617 ligand binding site [chemical binding]; other site 1184267002618 putative active site [active] 1184267002619 NAD(P) binding site [chemical binding]; other site 1184267002620 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 1184267002621 Competence protein; Region: Competence; pfam03772 1184267002622 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 1184267002623 DNA protecting protein DprA; Region: dprA; TIGR00732 1184267002624 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 1184267002625 Predicted permeases [General function prediction only]; Region: COG0795 1184267002626 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1184267002627 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 1184267002628 catalytic residues [active] 1184267002629 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1184267002630 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1184267002631 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1184267002632 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1184267002633 rod shape-determining protein MreC; Provisional; Region: PRK13922 1184267002634 rod shape-determining protein MreC; Region: MreC; pfam04085 1184267002635 SurA N-terminal domain; Region: SurA_N_3; cl07813 1184267002636 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1184267002637 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1184267002638 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 1184267002639 active site 1184267002640 catalytic motif [active] 1184267002641 Zn binding site [ion binding]; other site 1184267002642 Maf-like protein; Region: Maf; pfam02545 1184267002643 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 1184267002644 active site 1184267002645 dimer interface [polypeptide binding]; other site 1184267002646 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 1184267002647 metal binding site 2 [ion binding]; metal-binding site 1184267002648 putative DNA binding helix; other site 1184267002649 metal binding site 1 [ion binding]; metal-binding site 1184267002650 dimer interface [polypeptide binding]; other site 1184267002651 structural Zn2+ binding site [ion binding]; other site 1184267002652 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 1184267002653 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1184267002654 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1184267002655 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1184267002656 hypothetical protein; Provisional; Region: PRK14013 1184267002657 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1184267002658 EamA-like transporter family; Region: EamA; pfam00892 1184267002659 FMN reductase; Validated; Region: fre; PRK08051 1184267002660 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cd00322 1184267002661 FAD binding pocket [chemical binding]; other site 1184267002662 conserved FAD binding motif [chemical binding]; other site 1184267002663 phosphate binding motif [ion binding]; other site 1184267002664 beta-alpha-beta structure motif; other site 1184267002665 NAD binding pocket [chemical binding]; other site 1184267002666 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 1184267002667 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267002668 Zn2+ binding site [ion binding]; other site 1184267002669 Mg2+ binding site [ion binding]; other site 1184267002670 Domain of unknown function (DUF1338); Region: DUF1338; pfam07063 1184267002671 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1184267002672 trimer interface [polypeptide binding]; other site 1184267002673 active site 1184267002674 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 1184267002675 Protein of unknown function, DUF399; Region: DUF399; pfam04187 1184267002676 AAA domain; Region: AAA_28; pfam13521 1184267002677 AAA domain; Region: AAA_17; cl17253 1184267002678 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 1184267002679 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1184267002680 intersubunit interface [polypeptide binding]; other site 1184267002681 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 1184267002682 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1184267002683 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1184267002684 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 1184267002685 putative active site [active] 1184267002686 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 1184267002687 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 1184267002688 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 1184267002689 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267002690 putative catalytic site [active] 1184267002691 putative metal binding site [ion binding]; other site 1184267002692 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267002693 putative catalytic site [active] 1184267002694 putative phosphate binding site [ion binding]; other site 1184267002695 putative phosphate binding site [ion binding]; other site 1184267002696 putative metal binding site [ion binding]; other site 1184267002697 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1184267002698 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1184267002699 active site 1184267002700 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1184267002701 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1184267002702 hydroxymethylglutaryl-CoA synthase; Region: PLN02577 1184267002703 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1184267002704 active site 1184267002705 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 1184267002706 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 1184267002707 putative ATP binding site [chemical binding]; other site 1184267002708 putative substrate interface [chemical binding]; other site 1184267002709 Deoxyhypusine synthase; Region: DS; cl00826 1184267002710 deoxyhypusine synthase; Region: dhys; TIGR00321 1184267002711 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1184267002712 PLD-like domain; Region: PLDc_2; pfam13091 1184267002713 putative active site [active] 1184267002714 catalytic site [active] 1184267002715 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 1184267002716 PLD-like domain; Region: PLDc_2; pfam13091 1184267002717 putative active site [active] 1184267002718 catalytic site [active] 1184267002719 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 1184267002720 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1184267002721 fructose-bisphosphate aldolase; Provisional; Region: PRK09250 1184267002722 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 1184267002723 putative active site; other site 1184267002724 catalytic residue [active] 1184267002725 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 1184267002726 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 1184267002727 dimer interface [polypeptide binding]; other site 1184267002728 putative anticodon binding site; other site 1184267002729 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 1184267002730 motif 1; other site 1184267002731 active site 1184267002732 motif 2; other site 1184267002733 motif 3; other site 1184267002734 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 1184267002735 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 1184267002736 active site 1184267002737 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 1184267002738 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267002739 Zn2+ binding site [ion binding]; other site 1184267002740 Mg2+ binding site [ion binding]; other site 1184267002741 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 1184267002742 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 1184267002743 ssDNA binding site; other site 1184267002744 generic binding surface II; other site 1184267002745 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 1184267002746 ATP binding site [chemical binding]; other site 1184267002747 putative Mg++ binding site [ion binding]; other site 1184267002748 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 1184267002749 nucleotide binding region [chemical binding]; other site 1184267002750 ATP-binding site [chemical binding]; other site 1184267002751 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 1184267002752 DNA photolyase; Region: DNA_photolyase; pfam00875 1184267002753 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 1184267002754 Peptidase S8 family domain in Kp43 proteases; Region: Peptidases_S8_Kp43_protease; cd04842 1184267002755 active site 1184267002756 catalytic triad [active] 1184267002757 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 1184267002758 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 1184267002759 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1184267002760 HIGH motif; other site 1184267002761 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1184267002762 active site 1184267002763 KMSKS motif; other site 1184267002764 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1184267002765 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1184267002766 active site 1184267002767 HIGH motif; other site 1184267002768 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1184267002769 KMSKS motif; other site 1184267002770 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1184267002771 tRNA binding surface [nucleotide binding]; other site 1184267002772 anticodon binding site; other site 1184267002773 Domain of unknown function(DUF2779); Region: DUF2779; pfam11074 1184267002774 Tryptophan 2,3-dioxygenase; Region: Trp_dioxygenase; cl03994 1184267002775 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1184267002776 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 1184267002777 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1184267002778 catalytic residue [active] 1184267002779 excinuclease ABC subunit B; Provisional; Region: PRK05298 1184267002780 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 1184267002781 ATP binding site [chemical binding]; other site 1184267002782 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 1184267002783 nucleotide binding region [chemical binding]; other site 1184267002784 ATP-binding site [chemical binding]; other site 1184267002785 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1184267002786 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1184267002787 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1184267002788 GIY-YIG motif/motif A; other site 1184267002789 active site 1184267002790 catalytic site [active] 1184267002791 putative DNA binding site [nucleotide binding]; other site 1184267002792 metal binding site [ion binding]; metal-binding site 1184267002793 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1184267002794 AMP nucleosidase; Provisional; Region: PRK07115 1184267002795 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 1184267002796 Stage II sporulation protein; Region: SpoIID; pfam08486 1184267002797 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 1184267002798 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 1184267002799 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 1184267002800 active site 1184267002801 Int/Topo IB signature motif; other site 1184267002802 DNA binding site [nucleotide binding] 1184267002803 Mg chelatase-related protein; Region: TIGR00368 1184267002804 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1184267002805 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1184267002806 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 1184267002807 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1184267002808 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 1184267002809 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1184267002810 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 1184267002811 ATP binding site [chemical binding]; other site 1184267002812 putative Mg++ binding site [ion binding]; other site 1184267002813 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 1184267002814 nucleotide binding region [chemical binding]; other site 1184267002815 ATP-binding site [chemical binding]; other site 1184267002816 HRDC domain; Region: HRDC; pfam00570 1184267002817 BioY family; Region: BioY; pfam02632 1184267002818 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 1184267002819 D-alanine-D-alanine ligase and related ATP-grasp enzymes [Cell envelope biogenesis, outer membrane]; Region: DdlA; COG1181 1184267002820 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1184267002821 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 1184267002822 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 1184267002823 active site 1184267002824 Zn binding site [ion binding]; other site 1184267002825 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 1184267002826 active site 1184267002827 catalytic residues [active] 1184267002828 PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase. This group contains various PA domain-containing proteins similar to S. pyogenes C5a, including, i) Vpr, a minor extracellular serine protease from...; Region: PA_C5a_like; cd02133 1184267002829 putative integrin binding motif; other site 1184267002830 PA/protease domain interface [polypeptide binding]; other site 1184267002831 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 1184267002832 catalytic residues [active] 1184267002833 RDD family; Region: RDD; pfam06271 1184267002834 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 1184267002835 active site 1184267002836 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1184267002837 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 1184267002838 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 1184267002839 FMN binding site [chemical binding]; other site 1184267002840 substrate binding site [chemical binding]; other site 1184267002841 putative catalytic residue [active] 1184267002842 HflK protein; Region: hflK; TIGR01933 1184267002843 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06676 1184267002844 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 1184267002845 RNA binding site [nucleotide binding]; other site 1184267002846 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 1184267002847 RNA binding site [nucleotide binding]; other site 1184267002848 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 1184267002849 RNA binding site [nucleotide binding]; other site 1184267002850 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cd00164 1184267002851 RNA binding site [nucleotide binding]; other site 1184267002852 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 1184267002853 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 1184267002854 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1184267002855 Methyltransferase domain; Region: Methyltransf_32; pfam13679 1184267002856 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1184267002857 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1184267002858 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11552 1184267002859 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1184267002860 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1184267002861 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1184267002862 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1184267002863 hypothetical protein; Validated; Region: PRK00029 1184267002864 Uncharacterized conserved protein [Function unknown]; Region: COG0397 1184267002865 High potential iron-sulfur protein; Region: HIPIP; pfam01355 1184267002866 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 1184267002867 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 1184267002868 acyl-activating enzyme (AAE) consensus motif; other site 1184267002869 putative AMP binding site [chemical binding]; other site 1184267002870 putative active site [active] 1184267002871 putative CoA binding site [chemical binding]; other site 1184267002872 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 1184267002873 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1184267002874 catalytic triad [active] 1184267002875 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 1184267002876 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 1184267002877 tetramer interface [polypeptide binding]; other site 1184267002878 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267002879 catalytic residue [active] 1184267002880 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 1184267002881 putative active site [active] 1184267002882 putative metal binding site [ion binding]; other site 1184267002883 epoxyqueuosine reductase; Region: TIGR00276 1184267002884 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 1184267002885 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1184267002886 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1184267002887 active site 1184267002888 NTP binding site [chemical binding]; other site 1184267002889 metal binding triad [ion binding]; metal-binding site 1184267002890 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1184267002891 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1184267002892 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 1184267002893 DNA binding residues [nucleotide binding] 1184267002894 dimerization interface [polypeptide binding]; other site 1184267002895 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 1184267002896 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 1184267002897 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 1184267002898 HflX GTPase family; Region: HflX; cd01878 1184267002899 G1 box; other site 1184267002900 GTP/Mg2+ binding site [chemical binding]; other site 1184267002901 Switch I region; other site 1184267002902 G2 box; other site 1184267002903 G3 box; other site 1184267002904 Switch II region; other site 1184267002905 G4 box; other site 1184267002906 G5 box; other site 1184267002907 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1184267002908 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1184267002909 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1184267002910 putative NAD(P) binding site [chemical binding]; other site 1184267002911 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 1184267002912 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 1184267002913 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 1184267002914 dimer interface [polypeptide binding]; other site 1184267002915 active site 1184267002916 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 1184267002917 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 1184267002918 substrate binding site [chemical binding]; other site 1184267002919 oxyanion hole (OAH) forming residues; other site 1184267002920 trimer interface [polypeptide binding]; other site 1184267002921 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1184267002922 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1184267002923 lipoprotein signal peptidase; Provisional; Region: PRK14787 1184267002924 Signal peptidase (SPase) II; Region: Peptidase_A8; pfam01252 1184267002925 FecR protein; Region: FecR; pfam04773 1184267002926 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 1184267002927 binding surface 1184267002928 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1184267002929 TPR motif; other site 1184267002930 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1184267002931 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 1184267002932 CHASE2 domain; Region: CHASE2; pfam05226 1184267002933 CHASE2 domain; Region: CHASE2; pfam05226 1184267002934 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 1184267002935 cyclase homology domain; Region: CHD; cd07302 1184267002936 nucleotidyl binding site; other site 1184267002937 metal binding site [ion binding]; metal-binding site 1184267002938 dimer interface [polypeptide binding]; other site 1184267002939 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1184267002940 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1184267002941 putative acyl-acceptor binding pocket; other site 1184267002942 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 1184267002943 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1184267002944 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 1184267002945 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 1184267002946 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 1184267002947 substrate binding site [chemical binding]; other site 1184267002948 oxyanion hole (OAH) forming residues; other site 1184267002949 trimer interface [polypeptide binding]; other site 1184267002950 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 1184267002951 B12 binding site [chemical binding]; other site 1184267002952 cobalt ligand [ion binding]; other site 1184267002953 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 1184267002954 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 1184267002955 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 1184267002956 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1184267002957 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 1184267002958 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1184267002959 catalytic residue [active] 1184267002960 helicase 45; Provisional; Region: PTZ00424 1184267002961 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 1184267002962 ATP binding site [chemical binding]; other site 1184267002963 Mg++ binding site [ion binding]; other site 1184267002964 motif III; other site 1184267002965 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 1184267002966 nucleotide binding region [chemical binding]; other site 1184267002967 ATP-binding site [chemical binding]; other site 1184267002968 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 1184267002969 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1184267002970 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 1184267002971 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 1184267002972 active site 1184267002973 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 1184267002974 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 1184267002975 dinuclear metal binding motif [ion binding]; other site 1184267002976 FeoA domain; Region: FeoA; pfam04023 1184267002977 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 1184267002978 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1184267002979 G1 box; other site 1184267002980 GTP/Mg2+ binding site [chemical binding]; other site 1184267002981 G2 box; other site 1184267002982 Switch I region; other site 1184267002983 G3 box; other site 1184267002984 Switch II region; other site 1184267002985 G4 box; other site 1184267002986 G5 box; other site 1184267002987 Nucleoside recognition; Region: Gate; pfam07670 1184267002988 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 1184267002989 Nucleoside recognition; Region: Gate; pfam07670 1184267002990 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 1184267002991 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 1184267002992 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 1184267002993 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 1184267002994 putative active site [active] 1184267002995 putative metal binding site [ion binding]; other site 1184267002996 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 1184267002997 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1184267002998 ligand binding site [chemical binding]; other site 1184267002999 flexible hinge region; other site 1184267003000 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 1184267003001 Peptidase family M48; Region: Peptidase_M48; pfam01435 1184267003002 M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica aminopeptidase; Region: M28_AAP; cd03879 1184267003003 Peptidase family M28; Region: Peptidase_M28; pfam04389 1184267003004 active site 1184267003005 metal binding site [ion binding]; metal-binding site 1184267003006 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1184267003007 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1184267003008 TrkA-C domain; Region: TrkA_C; pfam02080 1184267003009 TrkA-C domain; Region: TrkA_C; pfam02080 1184267003010 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 1184267003011 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1184267003012 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 1184267003013 homotrimer interaction site [polypeptide binding]; other site 1184267003014 putative active site [active] 1184267003015 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 1184267003016 putative active site [active] 1184267003017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267003018 Walker A/P-loop; other site 1184267003019 ATP binding site [chemical binding]; other site 1184267003020 ABC transporter; Region: ABC_tran; pfam00005 1184267003021 Q-loop/lid; other site 1184267003022 ABC transporter signature motif; other site 1184267003023 Walker B; other site 1184267003024 D-loop; other site 1184267003025 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 1184267003026 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1184267003027 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 1184267003028 trimer interface [polypeptide binding]; other site 1184267003029 active site 1184267003030 substrate binding site [chemical binding]; other site 1184267003031 CoA binding site [chemical binding]; other site 1184267003032 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 1184267003033 active site 1184267003034 Zn binding site [ion binding]; other site 1184267003035 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 1184267003036 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 1184267003037 active site 1184267003038 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1184267003039 substrate binding site [chemical binding]; other site 1184267003040 catalytic residues [active] 1184267003041 dimer interface [polypeptide binding]; other site 1184267003042 Penicillin-insensitive murein endopeptidase; Region: Peptidase_M74; cl01538 1184267003043 glutamate racemase; Provisional; Region: PRK00865 1184267003044 inosine 5-monophosphate dehydrogenase; Validated; Region: PRK06843 1184267003045 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 1184267003046 active site 1184267003047 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1184267003048 NAD(P) binding site [chemical binding]; other site 1184267003049 NADH(P)-binding; Region: NAD_binding_10; pfam13460 1184267003050 active site 1184267003051 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1184267003052 Coenzyme A binding pocket [chemical binding]; other site 1184267003053 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 1184267003054 active site 1184267003055 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 1184267003056 S-adenosylmethionine binding site [chemical binding]; other site 1184267003057 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 1184267003058 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 1184267003059 motif II; other site 1184267003060 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 1184267003061 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 1184267003062 NADP binding site [chemical binding]; other site 1184267003063 active site 1184267003064 steroid binding site; other site 1184267003065 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 1184267003066 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 1184267003067 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 1184267003068 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 1184267003069 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 1184267003070 rRNA binding site [nucleotide binding]; other site 1184267003071 predicted 30S ribosome binding site; other site 1184267003072 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 1184267003073 heme-binding site [chemical binding]; other site 1184267003074 NnrS protein; Region: NnrS; cl01258 1184267003075 NnrS protein; Region: NnrS; cl01258 1184267003076 Rrf2 family protein; Region: rrf2_super; TIGR00738 1184267003077 Transcriptional regulator; Region: Rrf2; cl17282 1184267003078 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1184267003079 Coenzyme A binding pocket [chemical binding]; other site 1184267003080 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 1184267003081 active site 1184267003082 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1184267003083 PLD-like domain; Region: PLDc_2; pfam13091 1184267003084 putative active site [active] 1184267003085 catalytic site [active] 1184267003086 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1184267003087 putative active site [active] 1184267003088 catalytic site [active] 1184267003089 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 1184267003090 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 1184267003091 Walker A/P-loop; other site 1184267003092 ATP binding site [chemical binding]; other site 1184267003093 Q-loop/lid; other site 1184267003094 ABC transporter signature motif; other site 1184267003095 Walker B; other site 1184267003096 D-loop; other site 1184267003097 H-loop/switch region; other site 1184267003098 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 1184267003099 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 1184267003100 dimer interface [polypeptide binding]; other site 1184267003101 conserved gate region; other site 1184267003102 putative PBP binding loops; other site 1184267003103 ABC-ATPase subunit interface; other site 1184267003104 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1184267003105 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 1184267003106 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267003107 putative catalytic site [active] 1184267003108 putative phosphate binding site [ion binding]; other site 1184267003109 putative metal binding site [ion binding]; other site 1184267003110 Uncharacterized conserved protein [Function unknown]; Region: COG3339 1184267003111 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267003112 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267003113 active site 1184267003114 phosphorylation site [posttranslational modification] 1184267003115 intermolecular recognition site; other site 1184267003116 dimerization interface [polypeptide binding]; other site 1184267003117 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1184267003118 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 1184267003119 ligand binding site [chemical binding]; other site 1184267003120 flexible hinge region; other site 1184267003121 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1184267003122 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1184267003123 active site 1184267003124 MltA-interacting protein MipA; Region: MipA; cl01504 1184267003125 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 1184267003126 Transposase; Region: DDE_Tnp_ISL3; pfam01610 1184267003127 BRICHOS domain; Region: BRICHOS; cl04394 1184267003128 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 1184267003129 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 1184267003130 Walker A motif; other site 1184267003131 ATP binding site [chemical binding]; other site 1184267003132 Walker B motif; other site 1184267003133 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 1184267003134 active site 1184267003135 Int/Topo IB signature motif; other site 1184267003136 DNA binding site [nucleotide binding] 1184267003137 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 1184267003138 DNA-binding interface [nucleotide binding]; DNA binding site 1184267003139 insertion element IS2 transposase InsD; Provisional; Region: PRK14702 1184267003140 HTH-like domain; Region: HTH_21; pfam13276 1184267003141 Integrase core domain; Region: rve; pfam00665 1184267003142 Integrase core domain; Region: rve_3; pfam13683 1184267003143 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 1184267003144 WYL domain; Region: WYL; pfam13280 1184267003145 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267003146 AAA domain; Region: AAA_23; pfam13476 1184267003147 Walker A/P-loop; other site 1184267003148 ATP binding site [chemical binding]; other site 1184267003149 Q-loop/lid; other site 1184267003150 AAA domain; Region: AAA_21; pfam13304 1184267003151 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 1184267003152 putative active site [active] 1184267003153 putative metal-binding site [ion binding]; other site 1184267003154 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 1184267003155 dimerization interface [polypeptide binding]; other site 1184267003156 putative active cleft [active] 1184267003157 Bacterial SH3 domain; Region: SH3_3; pfam08239 1184267003158 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1184267003159 Peptidase family M23; Region: Peptidase_M23; pfam01551 1184267003160 BON domain; Region: BON; pfam04972 1184267003161 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1184267003162 tRNA synthetases class I (M); Region: tRNA-synt_1g; pfam09334 1184267003163 active site 1184267003164 nucleotide binding site [chemical binding]; other site 1184267003165 HIGH motif; other site 1184267003166 KMSKS motif; other site 1184267003167 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1184267003168 anticodon binding site; other site 1184267003169 tRNA binding surface [nucleotide binding]; other site 1184267003170 16S rRNA methyltransferase B; Provisional; Region: PRK14902 1184267003171 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 1184267003172 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 1184267003173 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 1184267003174 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 1184267003175 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 1184267003176 FMN binding site [chemical binding]; other site 1184267003177 active site 1184267003178 substrate binding site [chemical binding]; other site 1184267003179 catalytic residue [active] 1184267003180 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267003181 putative catalytic site [active] 1184267003182 putative metal binding site [ion binding]; other site 1184267003183 putative phosphate binding site [ion binding]; other site 1184267003184 TIGR02147 family protein; Region: Fsuc_second 1184267003185 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 1184267003186 non-specific DNA binding site [nucleotide binding]; other site 1184267003187 salt bridge; other site 1184267003188 sequence-specific DNA binding site [nucleotide binding]; other site 1184267003189 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 1184267003190 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 1184267003191 motif II; other site 1184267003192 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 1184267003193 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1184267003194 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1184267003195 dimer interface [polypeptide binding]; other site 1184267003196 putative CheW interface [polypeptide binding]; other site 1184267003197 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267003198 Zn2+ binding site [ion binding]; other site 1184267003199 Mg2+ binding site [ion binding]; other site 1184267003200 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 1184267003201 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267003202 active site 1184267003203 phosphorylation site [posttranslational modification] 1184267003204 intermolecular recognition site; other site 1184267003205 dimerization interface [polypeptide binding]; other site 1184267003206 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 1184267003207 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 1184267003208 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 1184267003209 putative binding surface; other site 1184267003210 active site 1184267003211 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1184267003212 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 1184267003213 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 1184267003214 ATP binding site [chemical binding]; other site 1184267003215 Mg2+ binding site [ion binding]; other site 1184267003216 G-X-G motif; other site 1184267003217 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 1184267003218 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 1184267003219 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1184267003220 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1184267003221 dimer interface [polypeptide binding]; other site 1184267003222 putative CheW interface [polypeptide binding]; other site 1184267003223 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 1184267003224 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 1184267003225 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267003226 active site 1184267003227 phosphorylation site [posttranslational modification] 1184267003228 intermolecular recognition site; other site 1184267003229 dimerization interface [polypeptide binding]; other site 1184267003230 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 1184267003231 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267003232 active site 1184267003233 phosphorylation site [posttranslational modification] 1184267003234 intermolecular recognition site; other site 1184267003235 dimerization interface [polypeptide binding]; other site 1184267003236 CheB methylesterase; Region: CheB_methylest; pfam01339 1184267003237 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267003238 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267003239 active site 1184267003240 phosphorylation site [posttranslational modification] 1184267003241 intermolecular recognition site; other site 1184267003242 dimerization interface [polypeptide binding]; other site 1184267003243 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 1184267003244 DNA binding site [nucleotide binding] 1184267003245 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267003246 PAS domain; Region: PAS_9; pfam13426 1184267003247 putative active site [active] 1184267003248 heme pocket [chemical binding]; other site 1184267003249 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 1184267003250 dimer interface [polypeptide binding]; other site 1184267003251 phosphorylation site [posttranslational modification] 1184267003252 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 1184267003253 ATP binding site [chemical binding]; other site 1184267003254 Mg2+ binding site [ion binding]; other site 1184267003255 G-X-G motif; other site 1184267003256 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 1184267003257 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1184267003258 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1184267003259 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 1184267003260 ligand binding site [chemical binding]; other site 1184267003261 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1184267003262 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 1184267003263 ligand binding site [chemical binding]; other site 1184267003264 flexible hinge region; other site 1184267003265 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 1184267003266 putative peptidase; Provisional; Region: PRK11649 1184267003267 Peptidase family M23; Region: Peptidase_M23; pfam01551 1184267003268 CRP/FNR family transcriptional regulator; Provisional; Region: PRK13918 1184267003269 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 1184267003270 ligand binding site [chemical binding]; other site 1184267003271 flexible hinge region; other site 1184267003272 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 1184267003273 putative switch regulator; other site 1184267003274 non-specific DNA interactions [nucleotide binding]; other site 1184267003275 DNA binding site [nucleotide binding] 1184267003276 sequence specific DNA binding site [nucleotide binding]; other site 1184267003277 putative cAMP binding site [chemical binding]; other site 1184267003278 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1184267003279 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 1184267003280 metal-binding site [ion binding] 1184267003281 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1184267003282 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 1184267003283 motif II; other site 1184267003284 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 1184267003285 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 1184267003286 putative bifunctional cbb3-type cytochrome c oxidase subunit I/II; Provisional; Region: PRK14485 1184267003287 Low-spin heme binding site [chemical binding]; other site 1184267003288 Putative water exit pathway; other site 1184267003289 Binuclear center (active site) [active] 1184267003290 Putative proton exit pathway; other site 1184267003291 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 1184267003292 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 1184267003293 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1184267003294 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 1184267003295 4Fe-4S binding domain; Region: Fer4_5; pfam12801 1184267003296 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 1184267003297 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1184267003298 SlyX; Region: SlyX; pfam04102 1184267003299 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 1184267003300 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 1184267003301 Protein of unknown function DUF45; Region: DUF45; pfam01863 1184267003302 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1184267003303 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 1184267003304 S-adenosylmethionine binding site [chemical binding]; other site 1184267003305 Protein of unknown function (DUF3011); Region: DUF3011; pfam11218 1184267003306 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1184267003307 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1184267003308 active site 1184267003309 HIGH motif; other site 1184267003310 dimer interface [polypeptide binding]; other site 1184267003311 KMSKS motif; other site 1184267003312 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1184267003313 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267003314 active site 1184267003315 phosphorylation site [posttranslational modification] 1184267003316 intermolecular recognition site; other site 1184267003317 dimerization interface [polypeptide binding]; other site 1184267003318 Site-specific recombinase; Region: SpecificRecomb; cl15411 1184267003319 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1184267003320 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1184267003321 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1184267003322 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 1184267003323 active site 1184267003324 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1184267003325 aspartate kinase III; Validated; Region: PRK09084 1184267003326 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 1184267003327 nucleotide binding site [chemical binding]; other site 1184267003328 substrate binding site [chemical binding]; other site 1184267003329 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_1; cd04932 1184267003330 lysine allosteric regulatory site; other site 1184267003331 dimer interface [polypeptide binding]; other site 1184267003332 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 1184267003333 dimer interface [polypeptide binding]; other site 1184267003334 DNA polymerase IV; Reviewed; Region: PRK03103 1184267003335 Y-family of DNA polymerases; Region: PolY; cd00424 1184267003336 active site 1184267003337 DNA binding site [nucleotide binding] 1184267003338 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 1184267003339 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 1184267003340 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1184267003341 active site residue [active] 1184267003342 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 1184267003343 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 1184267003344 G1 box; other site 1184267003345 putative GEF interaction site [polypeptide binding]; other site 1184267003346 GTP/Mg2+ binding site [chemical binding]; other site 1184267003347 Switch I region; other site 1184267003348 G2 box; other site 1184267003349 G3 box; other site 1184267003350 Switch II region; other site 1184267003351 G4 box; other site 1184267003352 G5 box; other site 1184267003353 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 1184267003354 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1184267003355 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1184267003356 Walker A/P-loop; other site 1184267003357 ATP binding site [chemical binding]; other site 1184267003358 Q-loop/lid; other site 1184267003359 ABC transporter signature motif; other site 1184267003360 Walker B; other site 1184267003361 D-loop; other site 1184267003362 H-loop/switch region; other site 1184267003363 ABC-2 type transporter; Region: ABC2_membrane; cl17235 1184267003364 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 1184267003365 signal recognition particle protein; Provisional; Region: PRK10867 1184267003366 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1184267003367 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 1184267003368 P loop; other site 1184267003369 GTP binding site [chemical binding]; other site 1184267003370 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1184267003371 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1184267003372 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 1184267003373 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 1184267003374 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1184267003375 RimM N-terminal domain; Region: RimM; pfam01782 1184267003376 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 1184267003377 SAM-dependent RNA methyltransferase; Region: Methyltrn_RNA_4; pfam09936 1184267003378 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1184267003379 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1184267003380 RNA/DNA hybrid binding site [nucleotide binding]; other site 1184267003381 active site 1184267003382 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1184267003383 OstA-like protein; Region: OstA; cl00844 1184267003384 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1184267003385 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1184267003386 Vitamin K epoxide reductase family in bacteria; Region: VKOR_3; cd12920 1184267003387 putative active site [active] 1184267003388 redox center [active] 1184267003389 Thioredoxin; Region: Thioredoxin_4; cl17273 1184267003390 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1184267003391 Protein of unknown function, DUF399; Region: DUF399; cl01139 1184267003392 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 1184267003393 IHF - DNA interface [nucleotide binding]; other site 1184267003394 IHF dimer interface [polypeptide binding]; other site 1184267003395 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 1184267003396 pyruvate kinase; Provisional; Region: PRK05826 1184267003397 domain interfaces; other site 1184267003398 active site 1184267003399 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1184267003400 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1184267003401 putative acyltransferase; Provisional; Region: PRK05790 1184267003402 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 1184267003403 dimer interface [polypeptide binding]; other site 1184267003404 active site 1184267003405 YceI-like domain; Region: YceI; cl01001 1184267003406 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1184267003407 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1184267003408 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1184267003409 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 1184267003410 FeS/SAM binding site; other site 1184267003411 TRAM domain; Region: TRAM; pfam01938 1184267003412 Bifunctional nuclease; Region: DNase-RNase; cl00553 1184267003413 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 1184267003414 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 1184267003415 trimer interface [polypeptide binding]; other site 1184267003416 putative metal binding site [ion binding]; other site 1184267003417 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 1184267003418 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 1184267003419 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 1184267003420 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 1184267003421 active site 1184267003422 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 1184267003423 GMP synthase; Reviewed; Region: guaA; PRK00074 1184267003424 AMP/PPi binding site [chemical binding]; other site 1184267003425 candidate oxyanion hole; other site 1184267003426 catalytic triad [active] 1184267003427 potential glutamine specificity residues [chemical binding]; other site 1184267003428 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 1184267003429 ATP Binding subdomain [chemical binding]; other site 1184267003430 Ligand Binding sites [chemical binding]; other site 1184267003431 Dimerization subdomain; other site 1184267003432 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1184267003433 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 1184267003434 active site 1184267003435 PHP Thumb interface [polypeptide binding]; other site 1184267003436 metal binding site [ion binding]; metal-binding site 1184267003437 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 1184267003438 generic binding surface II; other site 1184267003439 generic binding surface I; other site 1184267003440 EDD domain protein, DegV family; Region: DegV; TIGR00762 1184267003441 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1184267003442 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 1184267003443 active site 1184267003444 catalytic residues [active] 1184267003445 Immunoglobulin I-set domain; Region: I-set; pfam07679 1184267003446 Immunoglobulin domain; Region: Ig_2; pfam13895 1184267003447 Family description; Region: DsbD_2; pfam13386 1184267003448 hypothetical protein; Provisional; Region: PRK09256 1184267003449 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1184267003450 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 1184267003451 NAD(P) binding site [chemical binding]; other site 1184267003452 catalytic residues [active] 1184267003453 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 1184267003454 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 1184267003455 Ligand Binding Site [chemical binding]; other site 1184267003456 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1184267003457 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1184267003458 PilZ domain; Region: PilZ; pfam07238 1184267003459 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 1184267003460 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 1184267003461 S-adenosylmethionine binding site [chemical binding]; other site 1184267003462 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1184267003463 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1184267003464 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1184267003465 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 1184267003466 PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain; Region: PA; cl08238 1184267003467 M28 Zn-Peptidases containing a PA domain insert and associated with a PDZ domain; Region: M28_like_PA_PDZ_associated; cd05663 1184267003468 Peptidase family M28; Region: Peptidase_M28; pfam04389 1184267003469 metal binding site [ion binding]; metal-binding site 1184267003470 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 1184267003471 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1184267003472 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 1184267003473 S-adenosylmethionine binding site [chemical binding]; other site 1184267003474 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 1184267003475 FeS/SAM binding site; other site 1184267003476 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 1184267003477 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 1184267003478 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 1184267003479 Trp docking motif [polypeptide binding]; other site 1184267003480 active site 1184267003481 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 1184267003482 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 1184267003483 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 1184267003484 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 1184267003485 NAD binding site [chemical binding]; other site 1184267003486 Phe binding site; other site 1184267003487 Putative 2OG-Fe(II) oxygenase; Region: 2OG-FeII_Oxy_5; cl17879 1184267003488 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 1184267003489 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 1184267003490 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1184267003491 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 1184267003492 dimer interface [polypeptide binding]; other site 1184267003493 active site 1184267003494 CoA binding pocket [chemical binding]; other site 1184267003495 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1184267003496 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1184267003497 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 1184267003498 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1184267003499 NAD(P) binding site [chemical binding]; other site 1184267003500 homotetramer interface [polypeptide binding]; other site 1184267003501 homodimer interface [polypeptide binding]; other site 1184267003502 active site 1184267003503 acyl carrier protein; Provisional; Region: acpP; PRK00982 1184267003504 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 1184267003505 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 1184267003506 dimer interface [polypeptide binding]; other site 1184267003507 active site 1184267003508 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 1184267003509 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 1184267003510 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1184267003511 dimer interface [polypeptide binding]; other site 1184267003512 active site 1184267003513 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1184267003514 folate binding site [chemical binding]; other site 1184267003515 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1184267003516 Peptidase family M23; Region: Peptidase_M23; pfam01551 1184267003517 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 1184267003518 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 1184267003519 active site 1184267003520 nucleophile elbow; other site 1184267003521 PilZ domain; Region: PilZ; pfam07238 1184267003522 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 1184267003523 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 1184267003524 ribonucleoside--diphosphate reductase large subunit; Region: PLN02437 1184267003525 ATP cone domain; Region: ATP-cone; pfam03477 1184267003526 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1184267003527 active site 1184267003528 dimer interface [polypeptide binding]; other site 1184267003529 catalytic residues [active] 1184267003530 effector binding site; other site 1184267003531 R2 peptide binding site; other site 1184267003532 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1184267003533 dimer interface [polypeptide binding]; other site 1184267003534 putative radical transfer pathway; other site 1184267003535 diiron center [ion binding]; other site 1184267003536 tyrosyl radical; other site 1184267003537 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 1184267003538 ScpA/B protein; Region: ScpA_ScpB; cl00598 1184267003539 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 1184267003540 Peptidase family M50; Region: Peptidase_M50; pfam02163 1184267003541 active site 1184267003542 putative substrate binding region [chemical binding]; other site 1184267003543 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 1184267003544 heme-binding site [chemical binding]; other site 1184267003545 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 1184267003546 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 1184267003547 FAD binding site [chemical binding]; other site 1184267003548 homotetramer interface [polypeptide binding]; other site 1184267003549 substrate binding pocket [chemical binding]; other site 1184267003550 catalytic base [active] 1184267003551 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 1184267003552 classical (c) SDRs; Region: SDR_c; cd05233 1184267003553 NAD(P) binding site [chemical binding]; other site 1184267003554 active site 1184267003555 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1184267003556 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 1184267003557 RNA binding surface [nucleotide binding]; other site 1184267003558 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1184267003559 active site 1184267003560 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 1184267003561 dinuclear metal binding motif [ion binding]; other site 1184267003562 Transcriptional regulator; Region: Transcrip_reg; pfam01709 1184267003563 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 1184267003564 Uncharacterized conserved protein (DUF2183); Region: DUF2183; pfam09949 1184267003565 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1184267003566 MutS domain I; Region: MutS_I; pfam01624 1184267003567 MutS domain III; Region: MutS_III; pfam05192 1184267003568 MutS domain V; Region: MutS_V; pfam00488 1184267003569 Walker A/P-loop; other site 1184267003570 ATP binding site [chemical binding]; other site 1184267003571 Q-loop/lid; other site 1184267003572 ABC transporter signature motif; other site 1184267003573 Walker B; other site 1184267003574 D-loop; other site 1184267003575 H-loop/switch region; other site 1184267003576 Predicted permeases [General function prediction only]; Region: RarD; COG2962 1184267003577 UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]; Region: MurC; COG0773 1184267003578 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1184267003579 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1184267003580 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1184267003581 Beta-lactamase; Region: Beta-lactamase; pfam00144 1184267003582 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1184267003583 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1184267003584 dimer interface [polypeptide binding]; other site 1184267003585 catalytic triad [active] 1184267003586 adenylosuccinate lyase; Provisional; Region: PRK07380 1184267003587 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 1184267003588 tetramer interface [polypeptide binding]; other site 1184267003589 active site 1184267003590 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 1184267003591 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 1184267003592 Na2 binding site [ion binding]; other site 1184267003593 putative substrate binding site 1 [chemical binding]; other site 1184267003594 Na binding site 1 [ion binding]; other site 1184267003595 putative substrate binding site 2 [chemical binding]; other site 1184267003596 ribosome-associated GTPase EngA; Region: GTPase_EngA; TIGR03594 1184267003597 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1184267003598 G1 box; other site 1184267003599 GTP/Mg2+ binding site [chemical binding]; other site 1184267003600 Switch I region; other site 1184267003601 G2 box; other site 1184267003602 Switch II region; other site 1184267003603 G3 box; other site 1184267003604 G4 box; other site 1184267003605 G5 box; other site 1184267003606 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1184267003607 G1 box; other site 1184267003608 GTP/Mg2+ binding site [chemical binding]; other site 1184267003609 Switch I region; other site 1184267003610 G2 box; other site 1184267003611 G3 box; other site 1184267003612 Switch II region; other site 1184267003613 G4 box; other site 1184267003614 G5 box; other site 1184267003615 GTPase Era; Reviewed; Region: era; PRK00089 1184267003616 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1184267003617 G1 box; other site 1184267003618 GTP/Mg2+ binding site [chemical binding]; other site 1184267003619 Switch I region; other site 1184267003620 G2 box; other site 1184267003621 Switch II region; other site 1184267003622 G3 box; other site 1184267003623 G4 box; other site 1184267003624 G5 box; other site 1184267003625 KH domain; Region: KH_2; pfam07650 1184267003626 ribonuclease III; Reviewed; Region: rnc; PRK00102 1184267003627 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 1184267003628 dimerization interface [polypeptide binding]; other site 1184267003629 active site 1184267003630 metal binding site [ion binding]; metal-binding site 1184267003631 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 1184267003632 dsRNA binding site [nucleotide binding]; other site 1184267003633 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1184267003634 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1184267003635 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 1184267003636 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 1184267003637 Ligand Binding Site [chemical binding]; other site 1184267003638 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1184267003639 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1184267003640 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1184267003641 catalytic residue [active] 1184267003642 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1184267003643 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 1184267003644 active site 1184267003645 hydrophilic channel; other site 1184267003646 dimerization interface [polypeptide binding]; other site 1184267003647 catalytic residues [active] 1184267003648 active site lid [active] 1184267003649 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14314 1184267003650 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 1184267003651 active site 1184267003652 substrate binding site [chemical binding]; other site 1184267003653 metal binding site [ion binding]; metal-binding site 1184267003654 YbbR-like protein; Region: YbbR; pfam07949 1184267003655 Uncharacterized conserved protein [Function unknown]; Region: COG1624 1184267003656 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 1184267003657 FtsH Extracellular; Region: FtsH_ext; pfam06480 1184267003658 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1184267003659 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 1184267003660 Walker A motif; other site 1184267003661 ATP binding site [chemical binding]; other site 1184267003662 Walker B motif; other site 1184267003663 arginine finger; other site 1184267003664 Peptidase family M41; Region: Peptidase_M41; pfam01434 1184267003665 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 1184267003666 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1184267003667 Ligand Binding Site [chemical binding]; other site 1184267003668 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1184267003669 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1184267003670 NAD(P) binding site [chemical binding]; other site 1184267003671 catalytic residues [active] 1184267003672 Polyketide cyclase / dehydrase and lipid transport; Region: Polyketide_cyc; pfam03364 1184267003673 hydrophobic ligand binding site; other site 1184267003674 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 1184267003675 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 1184267003676 putative active site [active] 1184267003677 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 1184267003678 active site 1184267003679 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1184267003680 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 1184267003681 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267003682 Zn2+ binding site [ion binding]; other site 1184267003683 Mg2+ binding site [ion binding]; other site 1184267003684 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 1184267003685 active site 1184267003686 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 1184267003687 galactosyl transferase GMA12/MNN10 family; Region: Glyco_transf_34; cl05288 1184267003688 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 1184267003689 Ligand binding site; other site 1184267003690 Putative Catalytic site; other site 1184267003691 DXD motif; other site 1184267003692 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1184267003693 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 1184267003694 active site 1184267003695 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 1184267003696 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 1184267003697 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1184267003698 active site 1184267003699 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 1184267003700 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1184267003701 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1184267003702 DNA binding site [nucleotide binding] 1184267003703 catalytic residue [active] 1184267003704 H2TH interface [polypeptide binding]; other site 1184267003705 putative catalytic residues [active] 1184267003706 turnover-facilitating residue; other site 1184267003707 intercalation triad [nucleotide binding]; other site 1184267003708 8OG recognition residue [nucleotide binding]; other site 1184267003709 putative reading head residues; other site 1184267003710 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1184267003711 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1184267003712 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 1184267003713 putative inner membrane peptidase; Provisional; Region: PRK11778 1184267003714 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1184267003715 tandem repeat interface [polypeptide binding]; other site 1184267003716 oligomer interface [polypeptide binding]; other site 1184267003717 active site residues [active] 1184267003718 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 1184267003719 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1184267003720 Walker A/P-loop; other site 1184267003721 ATP binding site [chemical binding]; other site 1184267003722 Q-loop/lid; other site 1184267003723 ABC transporter signature motif; other site 1184267003724 Walker B; other site 1184267003725 D-loop; other site 1184267003726 H-loop/switch region; other site 1184267003727 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1184267003728 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 1184267003729 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1184267003730 Walker A/P-loop; other site 1184267003731 ATP binding site [chemical binding]; other site 1184267003732 Q-loop/lid; other site 1184267003733 ABC transporter signature motif; other site 1184267003734 Walker B; other site 1184267003735 D-loop; other site 1184267003736 H-loop/switch region; other site 1184267003737 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 1184267003738 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1184267003739 The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold; Region: PBP2_thermophilic_Hb8_like; cd08513 1184267003740 peptide binding site [polypeptide binding]; other site 1184267003741 dimer interface [polypeptide binding]; other site 1184267003742 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1184267003743 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 1184267003744 dimer interface [polypeptide binding]; other site 1184267003745 conserved gate region; other site 1184267003746 putative PBP binding loops; other site 1184267003747 ABC-ATPase subunit interface; other site 1184267003748 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 1184267003749 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 1184267003750 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 1184267003751 dimer interface [polypeptide binding]; other site 1184267003752 conserved gate region; other site 1184267003753 putative PBP binding loops; other site 1184267003754 ABC-ATPase subunit interface; other site 1184267003755 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 1184267003756 Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]; Region: TatA; COG1826 1184267003757 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 1184267003758 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 1184267003759 active site 1184267003760 catalytic site [active] 1184267003761 metal binding site [ion binding]; metal-binding site 1184267003762 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1184267003763 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1184267003764 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1184267003765 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1184267003766 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 1184267003767 NAD(P) binding site [chemical binding]; other site 1184267003768 active site 1184267003769 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_3; cd07820 1184267003770 putative hydrophobic ligand binding site [chemical binding]; other site 1184267003771 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 1184267003772 ABC1 family; Region: ABC1; cl17513 1184267003773 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 1184267003774 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 1184267003775 Predicted thiol-disulfide oxidoreductase [General function prediction only]; Region: COG3011 1184267003776 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 1184267003777 active site 1184267003778 8-oxo-dGMP binding site [chemical binding]; other site 1184267003779 nudix motif; other site 1184267003780 metal binding site [ion binding]; metal-binding site 1184267003781 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 1184267003782 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 1184267003783 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 1184267003784 PhoU domain; Region: PhoU; pfam01895 1184267003785 Domain of unknown function (DUF366); Region: DUF366; cl00890 1184267003786 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 1184267003787 Ligand Binding Site [chemical binding]; other site 1184267003788 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1184267003789 DHH family; Region: DHH; pfam01368 1184267003790 DHHA1 domain; Region: DHHA1; pfam02272 1184267003791 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1184267003792 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1184267003793 Protein export membrane protein; Region: SecD_SecF; pfam02355 1184267003794 Preprotein translocase subunit SecD [Intracellular trafficking and secretion]; Region: SecD; COG0342 1184267003795 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1184267003796 Preprotein translocase subunit; Region: YajC; pfam02699 1184267003797 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1184267003798 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1184267003799 Queuosine biosynthesis protein; Region: Queuosine_synth; pfam02547 1184267003800 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1184267003801 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 1184267003802 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 1184267003803 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 1184267003804 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267003805 catalytic triad [active] 1184267003806 putative active site [active] 1184267003807 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 1184267003808 catalytic residue [active] 1184267003809 FOG: CBS domain [General function prediction only]; Region: COG0517 1184267003810 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 1184267003811 short chain dehydrogenase; Provisional; Region: PRK06914 1184267003812 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1184267003813 NAD(P) binding site [chemical binding]; other site 1184267003814 active site 1184267003815 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1184267003816 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cl00250 1184267003817 30S subunit binding site; other site 1184267003818 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1184267003819 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267003820 active site 1184267003821 phosphorylation site [posttranslational modification] 1184267003822 intermolecular recognition site; other site 1184267003823 dimerization interface [polypeptide binding]; other site 1184267003824 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 1184267003825 DNA binding site [nucleotide binding] 1184267003826 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 1184267003827 dimer interface [polypeptide binding]; other site 1184267003828 phosphorylation site [posttranslational modification] 1184267003829 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 1184267003830 ATP binding site [chemical binding]; other site 1184267003831 Mg2+ binding site [ion binding]; other site 1184267003832 G-X-G motif; other site 1184267003833 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267003834 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267003835 active site 1184267003836 phosphorylation site [posttranslational modification] 1184267003837 intermolecular recognition site; other site 1184267003838 dimerization interface [polypeptide binding]; other site 1184267003839 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1184267003840 Omptin family; Region: Omptin; cl01886 1184267003841 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 1184267003842 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 1184267003843 active site 1184267003844 Zn binding site [ion binding]; other site 1184267003845 Zn binding site [ion binding]; other site 1184267003846 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1184267003847 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1184267003848 putative metal binding site; other site 1184267003849 rod shape-determining protein MreB; Provisional; Region: PRK13930 1184267003850 MreB and similar proteins; Region: MreB_like; cd10225 1184267003851 nucleotide binding site [chemical binding]; other site 1184267003852 Mg binding site [ion binding]; other site 1184267003853 putative protofilament interaction site [polypeptide binding]; other site 1184267003854 RodZ interaction site [polypeptide binding]; other site 1184267003855 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 1184267003856 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1184267003857 active site 1184267003858 HIGH motif; other site 1184267003859 KMSKS motif; other site 1184267003860 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1184267003861 tRNA binding surface [nucleotide binding]; other site 1184267003862 anticodon binding site; other site 1184267003863 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 1184267003864 dimer interface [polypeptide binding]; other site 1184267003865 putative tRNA-binding site [nucleotide binding]; other site 1184267003866 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1184267003867 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 1184267003868 homodimer interaction site [polypeptide binding]; other site 1184267003869 cofactor binding site; other site 1184267003870 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 1184267003871 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 1184267003872 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1184267003873 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 1184267003874 dimer interface [polypeptide binding]; other site 1184267003875 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267003876 catalytic residue [active] 1184267003877 HipA N-terminal domain; Region: Couple_hipA; pfam13657 1184267003878 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 1184267003879 HipA-like N-terminal domain; Region: HipA_N; pfam07805 1184267003880 HipA-like C-terminal domain; Region: HipA_C; pfam07804 1184267003881 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1184267003882 sequence-specific DNA binding site [nucleotide binding]; other site 1184267003883 salt bridge; other site 1184267003884 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1184267003885 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 1184267003886 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 1184267003887 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 1184267003888 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1184267003889 NAD(P) binding site [chemical binding]; other site 1184267003890 active site 1184267003891 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 1184267003892 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1184267003893 NAD(P) binding site [chemical binding]; other site 1184267003894 homodimer interface [polypeptide binding]; other site 1184267003895 substrate binding site [chemical binding]; other site 1184267003896 active site 1184267003897 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1184267003898 O-Antigen ligase; Region: Wzy_C; pfam04932 1184267003899 Bacterial sugar transferase; Region: Bac_transf; pfam02397 1184267003900 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 1184267003901 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 1184267003902 inhibitor-cofactor binding pocket; inhibition site 1184267003903 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267003904 catalytic residue [active] 1184267003905 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 1184267003906 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1184267003907 putative ADP-binding pocket [chemical binding]; other site 1184267003908 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 1184267003909 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 1184267003910 putative trimer interface [polypeptide binding]; other site 1184267003911 putative CoA binding site [chemical binding]; other site 1184267003912 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 1184267003913 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 1184267003914 Ligand binding site; other site 1184267003915 Putative Catalytic site; other site 1184267003916 DXD motif; other site 1184267003917 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1184267003918 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 1184267003919 active site 1184267003920 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_10; cd13125 1184267003921 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 1184267003922 active site 1184267003923 cosubstrate binding site; other site 1184267003924 substrate binding site [chemical binding]; other site 1184267003925 catalytic site [active] 1184267003926 Carboxy-terminal domain of Formyltransferase and similar domains; Region: FMT_C_like; cl14785 1184267003927 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 1184267003928 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 1184267003929 inhibitor-cofactor binding pocket; inhibition site 1184267003930 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267003931 catalytic residue [active] 1184267003932 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 1184267003933 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 1184267003934 substrate binding site; other site 1184267003935 tetramer interface; other site 1184267003936 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 1184267003937 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 1184267003938 NAD binding site [chemical binding]; other site 1184267003939 substrate binding site [chemical binding]; other site 1184267003940 homodimer interface [polypeptide binding]; other site 1184267003941 active site 1184267003942 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1184267003943 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1184267003944 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 1184267003945 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 1184267003946 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1184267003947 NAD(P) binding site [chemical binding]; other site 1184267003948 active site 1184267003949 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 1184267003950 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 1184267003951 non-specific DNA binding site [nucleotide binding]; other site 1184267003952 salt bridge; other site 1184267003953 sequence-specific DNA binding site [nucleotide binding]; other site 1184267003954 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 1184267003955 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 1184267003956 active site 1184267003957 tetramer interface; other site 1184267003958 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 1184267003959 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 1184267003960 Walker A/P-loop; other site 1184267003961 ATP binding site [chemical binding]; other site 1184267003962 Q-loop/lid; other site 1184267003963 ABC transporter signature motif; other site 1184267003964 Walker B; other site 1184267003965 D-loop; other site 1184267003966 H-loop/switch region; other site 1184267003967 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 1184267003968 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 1184267003969 dimer interface [polypeptide binding]; other site 1184267003970 conserved gate region; other site 1184267003971 putative PBP binding loops; other site 1184267003972 ABC-ATPase subunit interface; other site 1184267003973 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 1184267003974 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 1184267003975 dimer interface [polypeptide binding]; other site 1184267003976 conserved gate region; other site 1184267003977 putative PBP binding loops; other site 1184267003978 ABC-ATPase subunit interface; other site 1184267003979 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 1184267003980 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 1184267003981 Substrate binding site; other site 1184267003982 Cupin domain; Region: Cupin_2; cl17218 1184267003983 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 1184267003984 dimer interface [polypeptide binding]; other site 1184267003985 phosphorylation site [posttranslational modification] 1184267003986 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 1184267003987 ATP binding site [chemical binding]; other site 1184267003988 Mg2+ binding site [ion binding]; other site 1184267003989 G-X-G motif; other site 1184267003990 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 1184267003991 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 1184267003992 DNA binding residues [nucleotide binding] 1184267003993 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 1184267003994 IHF dimer interface [polypeptide binding]; other site 1184267003995 IHF - DNA interface [nucleotide binding]; other site 1184267003996 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1184267003997 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 1184267003998 putative tRNA-binding site [nucleotide binding]; other site 1184267003999 B3/4 domain; Region: B3_4; pfam03483 1184267004000 tRNA synthetase B5 domain; Region: B5; pfam03484 1184267004001 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 1184267004002 dimer interface [polypeptide binding]; other site 1184267004003 motif 1; other site 1184267004004 motif 3; other site 1184267004005 motif 2; other site 1184267004006 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1184267004007 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1184267004008 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1184267004009 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 1184267004010 dimer interface [polypeptide binding]; other site 1184267004011 motif 1; other site 1184267004012 active site 1184267004013 motif 2; other site 1184267004014 motif 3; other site 1184267004015 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1184267004016 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; cl17726 1184267004017 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1184267004018 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1184267004019 RNA polymerase subunit; Provisional; Region: PHA02998 1184267004020 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 1184267004021 Ligand binding site; other site 1184267004022 Putative Catalytic site; other site 1184267004023 DXD motif; other site 1184267004024 mevalonate kinase; Region: mevalon_kin; TIGR00549 1184267004025 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 1184267004026 diphosphomevalonate decarboxylase; Region: PLN02407 1184267004027 diphosphomevalonate decarboxylase; Region: mevDPdecarb; TIGR01240 1184267004028 Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classII; cd00644 1184267004029 homodimer interface [polypeptide binding]; other site 1184267004030 catalytic residues [active] 1184267004031 NAD binding site [chemical binding]; other site 1184267004032 substrate binding pocket [chemical binding]; other site 1184267004033 flexible flap; other site 1184267004034 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1184267004035 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 1184267004036 homotetramer interface [polypeptide binding]; other site 1184267004037 FMN binding site [chemical binding]; other site 1184267004038 homodimer contacts [polypeptide binding]; other site 1184267004039 putative active site [active] 1184267004040 putative substrate binding site [chemical binding]; other site 1184267004041 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1184267004042 23S rRNA binding site [nucleotide binding]; other site 1184267004043 L21 binding site [polypeptide binding]; other site 1184267004044 L13 binding site [polypeptide binding]; other site 1184267004045 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1184267004046 Domain of unknown function (DUF4156); Region: DUF4156; pfam13698 1184267004047 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1184267004048 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1184267004049 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1184267004050 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1184267004051 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 1184267004052 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 1184267004053 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 1184267004054 active site 1184267004055 dimer interface [polypeptide binding]; other site 1184267004056 motif 1; other site 1184267004057 motif 2; other site 1184267004058 motif 3; other site 1184267004059 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 1184267004060 anticodon binding site; other site 1184267004061 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1184267004062 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1184267004063 Protein of unknown function (DUF3341); Region: DUF3341; pfam11821 1184267004064 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 1184267004065 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 1184267004066 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 1184267004067 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 1184267004068 molybdopterin cofactor binding site; other site 1184267004069 The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region...; Region: MopB_CT_PHLH; cd02784 1184267004070 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 1184267004071 4Fe-4S binding domain; Region: Fer4; cl02805 1184267004072 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 1184267004073 heme-binding residues [chemical binding]; other site 1184267004074 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1184267004075 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 1184267004076 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 1184267004077 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 1184267004078 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 1184267004079 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 1184267004080 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 1184267004081 protein binding site [polypeptide binding]; other site 1184267004082 type II secretion system protein D; Region: type_II_gspD; TIGR02517 1184267004083 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1184267004084 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1184267004085 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 1184267004086 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1184267004087 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 1184267004088 type II secretion system protein E; Region: type_II_gspE; TIGR02533 1184267004089 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 1184267004090 Walker A motif; other site 1184267004091 ATP binding site [chemical binding]; other site 1184267004092 Walker B motif; other site 1184267004093 type II secretion system protein F; Region: GspF; TIGR02120 1184267004094 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1184267004095 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1184267004096 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 1184267004097 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 1184267004098 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 1184267004099 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 1184267004100 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 1184267004101 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 1184267004102 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 1184267004103 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 1184267004104 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 1184267004105 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 1184267004106 Competence protein A; Region: Competence_A; pfam11104 1184267004107 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1184267004108 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1184267004109 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 1184267004110 dimer interface [polypeptide binding]; other site 1184267004111 ssDNA binding site [nucleotide binding]; other site 1184267004112 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1184267004113 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1184267004114 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267004115 Zn2+ binding site [ion binding]; other site 1184267004116 Mg2+ binding site [ion binding]; other site 1184267004117 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1184267004118 synthetase active site [active] 1184267004119 NTP binding site [chemical binding]; other site 1184267004120 metal binding site [ion binding]; metal-binding site 1184267004121 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 1184267004122 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 1184267004123 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 1184267004124 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1184267004125 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 1184267004126 catalytic site [active] 1184267004127 G-X2-G-X-G-K; other site 1184267004128 hypothetical protein; Provisional; Region: PRK11820 1184267004129 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 1184267004130 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 1184267004131 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1184267004132 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1184267004133 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1184267004134 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 1184267004135 ATP binding site [chemical binding]; other site 1184267004136 Mg2+ binding site [ion binding]; other site 1184267004137 G-X-G motif; other site 1184267004138 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 1184267004139 ATP binding site [chemical binding]; other site 1184267004140 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1184267004141 Yip1 domain; Region: Yip1; pfam04893 1184267004142 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1184267004143 trimer interface [polypeptide binding]; other site 1184267004144 active site 1184267004145 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1184267004146 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1184267004147 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1184267004148 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1184267004149 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1184267004150 RNase E interface [polypeptide binding]; other site 1184267004151 trimer interface [polypeptide binding]; other site 1184267004152 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1184267004153 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1184267004154 RNase E interface [polypeptide binding]; other site 1184267004155 trimer interface [polypeptide binding]; other site 1184267004156 active site 1184267004157 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 1184267004158 putative nucleic acid binding region [nucleotide binding]; other site 1184267004159 G-X-X-G motif; other site 1184267004160 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 1184267004161 RNA binding site [nucleotide binding]; other site 1184267004162 domain interface; other site 1184267004163 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 1184267004164 16S/18S rRNA binding site [nucleotide binding]; other site 1184267004165 S13e-L30e interaction site [polypeptide binding]; other site 1184267004166 25S rRNA binding site [nucleotide binding]; other site 1184267004167 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 1184267004168 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1184267004169 RNA binding site [nucleotide binding]; other site 1184267004170 active site 1184267004171 Ribosome-binding factor A; Region: RBFA; pfam02033 1184267004172 translation initiation factor IF-2; Region: IF-2; TIGR00487 1184267004173 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1184267004174 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1184267004175 G1 box; other site 1184267004176 putative GEF interaction site [polypeptide binding]; other site 1184267004177 GTP/Mg2+ binding site [chemical binding]; other site 1184267004178 Switch I region; other site 1184267004179 G2 box; other site 1184267004180 G3 box; other site 1184267004181 Switch II region; other site 1184267004182 G4 box; other site 1184267004183 G5 box; other site 1184267004184 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 1184267004185 Translation-initiation factor 2; Region: IF-2; pfam11987 1184267004186 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 1184267004187 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 1184267004188 NusA N-terminal domain; Region: NusA_N; pfam08529 1184267004189 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 1184267004190 RNA binding site [nucleotide binding]; other site 1184267004191 homodimer interface [polypeptide binding]; other site 1184267004192 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 1184267004193 G-X-X-G motif; other site 1184267004194 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 1184267004195 G-X-X-G motif; other site 1184267004196 ribosome maturation protein RimP; Reviewed; Region: PRK00092 1184267004197 Sm and related proteins; Region: Sm_like; cl00259 1184267004198 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1184267004199 putative oligomer interface [polypeptide binding]; other site 1184267004200 putative RNA binding site [nucleotide binding]; other site 1184267004201 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 1184267004202 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1184267004203 Coenzyme A binding pocket [chemical binding]; other site 1184267004204 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 1184267004205 Beta-propeller repeat; Region: SBBP; pfam06739 1184267004206 Beta-propeller repeat; Region: SBBP; pfam06739 1184267004207 Beta-propeller repeat; Region: SBBP; pfam06739 1184267004208 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 1184267004209 TIGR02147 family protein; Region: Fsuc_second 1184267004210 non-specific DNA binding site [nucleotide binding]; other site 1184267004211 salt bridge; other site 1184267004212 sequence-specific DNA binding site [nucleotide binding]; other site 1184267004213 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1184267004214 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 1184267004215 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1184267004216 catalytic residue [active] 1184267004217 Domain of unknown function (DUF1768); Region: DUF1768; cl01271 1184267004218 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1184267004219 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1184267004220 active site 1184267004221 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1184267004222 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 1184267004223 S-adenosylmethionine binding site [chemical binding]; other site 1184267004224 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 1184267004225 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 1184267004226 putative substrate translocation pore; other site 1184267004227 Predicted transcriptional regulator [Transcription]; Region: COG1959 1184267004228 Transcriptional regulator; Region: Rrf2; pfam02082 1184267004229 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1184267004230 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1184267004231 active site 1184267004232 recombination factor protein RarA; Reviewed; Region: PRK13342 1184267004233 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 1184267004234 Walker A motif; other site 1184267004235 ATP binding site [chemical binding]; other site 1184267004236 Walker B motif; other site 1184267004237 arginine finger; other site 1184267004238 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 1184267004239 Protein of unknown function (DUF1304); Region: DUF1304; pfam06993 1184267004240 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 1184267004241 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 1184267004242 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 1184267004243 putative Mg++ binding site [ion binding]; other site 1184267004244 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 1184267004245 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 1184267004246 nucleotide binding region [chemical binding]; other site 1184267004247 ATP-binding site [chemical binding]; other site 1184267004248 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 1184267004249 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 1184267004250 putative active site [active] 1184267004251 putative metal binding site [ion binding]; other site 1184267004252 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1184267004253 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1184267004254 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 1184267004255 Walker A/P-loop; other site 1184267004256 ATP binding site [chemical binding]; other site 1184267004257 Q-loop/lid; other site 1184267004258 ABC transporter signature motif; other site 1184267004259 Walker B; other site 1184267004260 D-loop; other site 1184267004261 H-loop/switch region; other site 1184267004262 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 1184267004263 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 1184267004264 putative active site [active] 1184267004265 putative metal binding site [ion binding]; other site 1184267004266 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 1184267004267 AsnC family; Region: AsnC_trans_reg; pfam01037 1184267004268 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 1184267004269 Histidine kinase; Region: HisKA_3; pfam07730 1184267004270 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 1184267004271 ATP binding site [chemical binding]; other site 1184267004272 Mg2+ binding site [ion binding]; other site 1184267004273 G-X-G motif; other site 1184267004274 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1184267004275 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267004276 active site 1184267004277 phosphorylation site [posttranslational modification] 1184267004278 intermolecular recognition site; other site 1184267004279 dimerization interface [polypeptide binding]; other site 1184267004280 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 1184267004281 DNA binding residues [nucleotide binding] 1184267004282 dimerization interface [polypeptide binding]; other site 1184267004283 gamma-glutamyl kinase; Provisional; Region: PRK05429 1184267004284 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 1184267004285 nucleotide binding site [chemical binding]; other site 1184267004286 homotetrameric interface [polypeptide binding]; other site 1184267004287 putative phosphate binding site [ion binding]; other site 1184267004288 putative allosteric binding site; other site 1184267004289 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 1184267004290 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 1184267004291 putative catalytic cysteine [active] 1184267004292 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1184267004293 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 1184267004294 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 1184267004295 Low molecular weight phosphatase family; Region: LMWPc; cd00115 1184267004296 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 1184267004297 active site 1184267004298 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 1184267004299 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1184267004300 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 1184267004301 S-adenosylmethionine binding site [chemical binding]; other site 1184267004302 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 1184267004303 RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_II; cd03487 1184267004304 putative active site [active] 1184267004305 putative NTP binding site [chemical binding]; other site 1184267004306 putative nucleic acid binding site [nucleotide binding]; other site 1184267004307 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 1184267004308 catalytic site [active] 1184267004309 putative active site [active] 1184267004310 putative substrate binding site [chemical binding]; other site 1184267004311 dimer interface [polypeptide binding]; other site 1184267004312 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 1184267004313 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 1184267004314 homotetramer interface [polypeptide binding]; other site 1184267004315 ligand binding site [chemical binding]; other site 1184267004316 catalytic site [active] 1184267004317 NAD binding site [chemical binding]; other site 1184267004318 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 1184267004319 active site 1184267004320 SWI complex, BAF60b domains; Region: SWIB; smart00151 1184267004321 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; cl02542 1184267004322 HSP70 interaction site [polypeptide binding]; other site 1184267004323 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 1184267004324 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 1184267004325 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 1184267004326 FeS/SAM binding site; other site 1184267004327 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 1184267004328 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1184267004329 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267004330 Walker A/P-loop; other site 1184267004331 ATP binding site [chemical binding]; other site 1184267004332 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267004333 Q-loop/lid; other site 1184267004334 Q-loop/lid; other site 1184267004335 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267004336 ABC transporter signature motif; other site 1184267004337 Walker B; other site 1184267004338 ABC transporter; Region: ABC_tran_2; pfam12848 1184267004339 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267004340 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1184267004341 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1184267004342 active site 1184267004343 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1184267004344 Part of AAA domain; Region: AAA_19; pfam13245 1184267004345 Family description; Region: UvrD_C_2; pfam13538 1184267004346 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 1184267004347 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1184267004348 Class II fumarases; Region: Fumarase_classII; cd01362 1184267004349 active site 1184267004350 tetramer interface [polypeptide binding]; other site 1184267004351 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 1184267004352 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1184267004353 NAD(P) binding site [chemical binding]; other site 1184267004354 active site 1184267004355 EVE domain; Region: EVE; cl00728 1184267004356 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 1184267004357 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 1184267004358 FMN binding site [chemical binding]; other site 1184267004359 active site 1184267004360 catalytic residues [active] 1184267004361 substrate binding site [chemical binding]; other site 1184267004362 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 1184267004363 GSH binding site [chemical binding]; other site 1184267004364 catalytic residues [active] 1184267004365 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 1184267004366 FMN binding site [chemical binding]; other site 1184267004367 active site 1184267004368 catalytic residues [active] 1184267004369 substrate binding site [chemical binding]; other site 1184267004370 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 1184267004371 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1184267004372 acetyl-CoA synthetase; Provisional; Region: PRK00174 1184267004373 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 1184267004374 active site 1184267004375 CoA binding site [chemical binding]; other site 1184267004376 acyl-activating enzyme (AAE) consensus motif; other site 1184267004377 AMP binding site [chemical binding]; other site 1184267004378 acetate binding site [chemical binding]; other site 1184267004379 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1184267004380 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 1184267004381 nucleotide binding site [chemical binding]; other site 1184267004382 NEF interaction site [polypeptide binding]; other site 1184267004383 SBD interface [polypeptide binding]; other site 1184267004384 chaperone protein DnaJ; Provisional; Region: PRK10767 1184267004385 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 1184267004386 HSP70 interaction site [polypeptide binding]; other site 1184267004387 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1184267004388 Zn binding sites [ion binding]; other site 1184267004389 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1184267004390 dimer interface [polypeptide binding]; other site 1184267004391 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 1184267004392 Type IV pilin PilA; Region: Pilin_PilA; pfam14245 1184267004393 Uncharacterized conserved protein [Function unknown]; Region: COG2127 1184267004394 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 1184267004395 Clp amino terminal domain; Region: Clp_N; pfam02861 1184267004396 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 1184267004397 Walker A motif; other site 1184267004398 ATP binding site [chemical binding]; other site 1184267004399 Walker B motif; other site 1184267004400 arginine finger; other site 1184267004401 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 1184267004402 Walker A motif; other site 1184267004403 ATP binding site [chemical binding]; other site 1184267004404 Walker B motif; other site 1184267004405 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1184267004406 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1184267004407 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 1184267004408 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1184267004409 catalytic residue [active] 1184267004410 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267004411 catalytic triad [active] 1184267004412 putative active site [active] 1184267004413 apolipoprotein N-acyltransferase; Region: lnt; TIGR00546 1184267004414 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1184267004415 putative active site [active] 1184267004416 catalytic triad [active] 1184267004417 putative dimer interface [polypeptide binding]; other site 1184267004418 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 1184267004419 MutS domain III; Region: MutS_III; pfam05192 1184267004420 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267004421 Walker A/P-loop; other site 1184267004422 ATP binding site [chemical binding]; other site 1184267004423 Q-loop/lid; other site 1184267004424 ABC transporter signature motif; other site 1184267004425 Walker B; other site 1184267004426 D-loop; other site 1184267004427 H-loop/switch region; other site 1184267004428 Smr domain; Region: Smr; pfam01713 1184267004429 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 1184267004430 active site 1184267004431 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 1184267004432 tartrate dehydrogenase; Region: TTC; TIGR02089 1184267004433 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 1184267004434 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 1184267004435 dimerization interface [polypeptide binding]; other site 1184267004436 domain crossover interface; other site 1184267004437 redox-dependent activation switch; other site 1184267004438 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 1184267004439 catalytic core [active] 1184267004440 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 1184267004441 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 1184267004442 Proline dehydrogenase; Region: Pro_dh; cl03282 1184267004443 Delta(1)-pyrroline-5-carboxylate dehydrogenase, RocA; Region: ALDH_PutA-P5CDH-RocA; cd07124 1184267004444 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 1184267004445 Glutamate binding site [chemical binding]; other site 1184267004446 homodimer interface [polypeptide binding]; other site 1184267004447 NAD binding site [chemical binding]; other site 1184267004448 catalytic residues [active] 1184267004449 Rhomboid family; Region: Rhomboid; cl11446 1184267004450 RDD family; Region: RDD; pfam06271 1184267004451 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267004452 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 1184267004453 active site 1184267004454 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1184267004455 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 1184267004456 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 1184267004457 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1184267004458 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 1184267004459 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 1184267004460 putative active site [active] 1184267004461 ferrochelatase; Reviewed; Region: hemH; PRK00035 1184267004462 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 1184267004463 C-terminal domain interface [polypeptide binding]; other site 1184267004464 active site 1184267004465 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 1184267004466 active site 1184267004467 N-terminal domain interface [polypeptide binding]; other site 1184267004468 Protoporphyrinogen oxidase [Coenzyme metabolism]; Region: HemY; COG1232 1184267004469 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1184267004470 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 1184267004471 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 1184267004472 FeS/SAM binding site; other site 1184267004473 HemN C-terminal domain; Region: HemN_C; pfam06969 1184267004474 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 1184267004475 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1184267004476 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267004477 active site 1184267004478 phosphorylation site [posttranslational modification] 1184267004479 intermolecular recognition site; other site 1184267004480 dimerization interface [polypeptide binding]; other site 1184267004481 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 1184267004482 DNA binding site [nucleotide binding] 1184267004483 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267004484 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 1184267004485 ATP binding site [chemical binding]; other site 1184267004486 Mg2+ binding site [ion binding]; other site 1184267004487 G-X-G motif; other site 1184267004488 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 1184267004489 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 1184267004490 inhibitor-cofactor binding pocket; inhibition site 1184267004491 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267004492 catalytic residue [active] 1184267004493 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 1184267004494 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; cl17708 1184267004495 domain interfaces; other site 1184267004496 active site 1184267004497 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 1184267004498 NAD(P) binding pocket [chemical binding]; other site 1184267004499 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 1184267004500 dimer interface [polypeptide binding]; other site 1184267004501 allosteric magnesium binding site [ion binding]; other site 1184267004502 active site 1184267004503 aspartate-rich active site metal binding site; other site 1184267004504 Schiff base residues; other site 1184267004505 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 1184267004506 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1184267004507 Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile. CGH is present in a number of probiotic microbial organisms that...; Region: Ntn_CGH; cd01902 1184267004508 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 1184267004509 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 1184267004510 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 1184267004511 dimer interface [polypeptide binding]; other site 1184267004512 active site 1184267004513 metal binding site [ion binding]; metal-binding site 1184267004514 glutathione binding site [chemical binding]; other site 1184267004515 Repair protein; Region: Repair_PSII; cl01535 1184267004516 Repair protein; Region: Repair_PSII; pfam04536 1184267004517 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 1184267004518 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1184267004519 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1184267004520 active site 1184267004521 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1184267004522 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 1184267004523 S-adenosylmethionine binding site [chemical binding]; other site 1184267004524 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1184267004525 isovaleryl-CoA dehydrogenase; Provisional; Region: PTZ00461 1184267004526 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1184267004527 active site 1184267004528 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 1184267004529 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 1184267004530 putative MPT binding site; other site 1184267004531 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 1184267004532 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 1184267004533 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1184267004534 Peptidase M35 family; Region: M35_like; cl03449 1184267004535 active site 1184267004536 Zn binding site [ion binding]; other site 1184267004537 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 1184267004538 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 1184267004539 homodimer interface [polypeptide binding]; other site 1184267004540 substrate-cofactor binding pocket; other site 1184267004541 catalytic residue [active] 1184267004542 Class II vitamin B12-dependent ribonucleotide reductase; Region: Ribonuc_red_2_N; pfam08471 1184267004543 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 1184267004544 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 1184267004545 active site 1184267004546 dimer interface [polypeptide binding]; other site 1184267004547 effector binding site; other site 1184267004548 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 1184267004549 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1184267004550 Calx-beta domain; Region: Calx-beta; cl02522 1184267004551 Calx-beta domain; Region: Calx-beta; cl02522 1184267004552 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1184267004553 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 1184267004554 catalytic loop [active] 1184267004555 iron binding site [ion binding]; other site 1184267004556 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1184267004557 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1184267004558 active site 1184267004559 HIGH motif; other site 1184267004560 dimer interface [polypeptide binding]; other site 1184267004561 KMSKS motif; other site 1184267004562 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 1184267004563 RNA binding surface [nucleotide binding]; other site 1184267004564 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 1184267004565 phosphodiesterase; Provisional; Region: PRK12704 1184267004566 KH domain; Region: KH_1; pfam00013 1184267004567 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267004568 Zn2+ binding site [ion binding]; other site 1184267004569 Mg2+ binding site [ion binding]; other site 1184267004570 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1184267004571 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 1184267004572 Cell division protein ZapA; Region: ZapA; pfam05164 1184267004573 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1184267004574 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 1184267004575 P loop; other site 1184267004576 GTP binding site [chemical binding]; other site 1184267004577 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1184267004578 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 1184267004579 Walker A/P-loop; other site 1184267004580 ATP binding site [chemical binding]; other site 1184267004581 Q-loop/lid; other site 1184267004582 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 1184267004583 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 1184267004584 dimer interface [polypeptide binding]; other site 1184267004585 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 1184267004586 ABC transporter signature motif; other site 1184267004587 Walker B; other site 1184267004588 D-loop; other site 1184267004589 H-loop/switch region; other site 1184267004590 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 1184267004591 DNA polymerase III, delta subunit; Region: holA; TIGR01128 1184267004592 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 1184267004593 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1184267004594 catalytic residue [active] 1184267004595 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 1184267004596 ligand binding site [chemical binding]; other site 1184267004597 NAD binding site [chemical binding]; other site 1184267004598 dimerization interface [polypeptide binding]; other site 1184267004599 catalytic site [active] 1184267004600 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 1184267004601 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 1184267004602 GDP-binding site [chemical binding]; other site 1184267004603 ACT binding site; other site 1184267004604 IMP binding site; other site 1184267004605 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 1184267004606 YcfA-like protein; Region: YcfA; cl00752 1184267004607 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1184267004608 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 1184267004609 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 1184267004610 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 1184267004611 FeS/SAM binding site; other site 1184267004612 YHS domain; Region: YHS; pfam04945 1184267004613 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1184267004614 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1184267004615 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 1184267004616 motif II; other site 1184267004617 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 1184267004618 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1184267004619 ATP binding site [chemical binding]; other site 1184267004620 putative Mg++ binding site [ion binding]; other site 1184267004621 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 1184267004622 nucleotide binding region [chemical binding]; other site 1184267004623 ATP-binding site [chemical binding]; other site 1184267004624 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1184267004625 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 1184267004626 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 1184267004627 dimer interface [polypeptide binding]; other site 1184267004628 putative tRNA-binding site [nucleotide binding]; other site 1184267004629 Domain of unknown function DUF21; Region: DUF21; pfam01595 1184267004630 FOG: CBS domain [General function prediction only]; Region: COG0517 1184267004631 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 1184267004632 Exopolysaccharide synthesis, ExoD; Region: ExoD; pfam06055 1184267004633 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 1184267004634 metal-binding site [ion binding] 1184267004635 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 1184267004636 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1184267004637 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 1184267004638 DNA binding residues [nucleotide binding] 1184267004639 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267004640 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267004641 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 1184267004642 dimerization interface [polypeptide binding]; other site 1184267004643 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 1184267004644 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1184267004645 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 1184267004646 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 1184267004647 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 1184267004648 intersubunit interface [polypeptide binding]; other site 1184267004649 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 1184267004650 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 1184267004651 ABC-ATPase subunit interface; other site 1184267004652 dimer interface [polypeptide binding]; other site 1184267004653 putative PBP binding regions; other site 1184267004654 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 1184267004655 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 1184267004656 Walker A/P-loop; other site 1184267004657 ATP binding site [chemical binding]; other site 1184267004658 Q-loop/lid; other site 1184267004659 ABC transporter signature motif; other site 1184267004660 Walker B; other site 1184267004661 D-loop; other site 1184267004662 H-loop/switch region; other site 1184267004663 Protein of unknown function (DUF1634); Region: DUF1634; pfam07843 1184267004664 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1184267004665 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1184267004666 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1184267004667 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1184267004668 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1184267004669 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1184267004670 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1184267004671 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 1184267004672 catalytic core [active] 1184267004673 Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX)...; Region: ArsC_like; cd03036 1184267004674 ArsC family; Region: ArsC; pfam03960 1184267004675 putative ArsC-like catalytic residues; other site 1184267004676 putative TRX-like catalytic residues [active] 1184267004677 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 1184267004678 AAA domain; Region: AAA_33; pfam13671 1184267004679 ATP-binding site [chemical binding]; other site 1184267004680 Sugar specificity; other site 1184267004681 Pyrimidine base specificity; other site 1184267004682 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1184267004683 active site 1184267004684 Protein of unknown function (DUF1688); Region: DUF1688; pfam07958 1184267004685 hypothetical protein; Validated; Region: PRK07198 1184267004686 GTP cyclohydrolase N terminal; Region: GTP_CH_N; pfam12471 1184267004687 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 1184267004688 dimerization interface [polypeptide binding]; other site 1184267004689 active site 1184267004690 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 1184267004691 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1184267004692 tetrameric interface [polypeptide binding]; other site 1184267004693 NAD binding site [chemical binding]; other site 1184267004694 catalytic residues [active] 1184267004695 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 1184267004696 S1 domain; Region: S1_2; pfam13509 1184267004697 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 1184267004698 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1184267004699 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 1184267004700 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1184267004701 active site 1184267004702 metal binding site [ion binding]; metal-binding site 1184267004703 PBP superfamily domain; Region: PBP_like_2; cl17296 1184267004704 Uncharacterized protein conserved in bacteria N-term (DUF3322); Region: DUF3322; pfam11795 1184267004705 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4924 1184267004706 Uncharacterized protein conserved in bacteria C-term(DUF2220); Region: DUF2220; pfam09983 1184267004707 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4913 1184267004708 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 1184267004709 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 1184267004710 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 1184267004711 Protein of unknown function (DUF3375); Region: DUF3375; pfam11855 1184267004712 ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation; Region: ASCH; cl01020 1184267004713 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 1184267004714 Family description; Region: DsbD_2; pfam13386 1184267004715 Predicted ATPase [General function prediction only]; Region: COG3911 1184267004716 AAA domain; Region: AAA_28; pfam13521 1184267004717 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 1184267004718 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 1184267004719 dimer interface [polypeptide binding]; other site 1184267004720 active site 1184267004721 Sucrose-6F-phosphate phosphohydrolase; Region: S6PP; pfam05116 1184267004722 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 1184267004723 active site 1184267004724 motif I; other site 1184267004725 motif II; other site 1184267004726 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 1184267004727 glucosylglycerol-phosphate synthase; Region: gluc_glyc_Psyn; TIGR02398 1184267004728 active site 1184267004729 homotetramer interface [polypeptide binding]; other site 1184267004730 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1184267004731 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 1184267004732 putative active site [active] 1184267004733 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 1184267004734 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1184267004735 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1184267004736 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1184267004737 Threonine/homoserine efflux transporter [Amino acid transport and metabolism]; Region: rhtA; COG5006 1184267004738 EamA-like transporter family; Region: EamA; pfam00892 1184267004739 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267004740 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 1184267004741 dimer interface [polypeptide binding]; other site 1184267004742 phosphorylation site [posttranslational modification] 1184267004743 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 1184267004744 ATP binding site [chemical binding]; other site 1184267004745 Mg2+ binding site [ion binding]; other site 1184267004746 G-X-G motif; other site 1184267004747 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267004748 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267004749 active site 1184267004750 phosphorylation site [posttranslational modification] 1184267004751 intermolecular recognition site; other site 1184267004752 dimerization interface [polypeptide binding]; other site 1184267004753 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1184267004754 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267004755 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1184267004756 putative lipoprotein, rSAM/lipoprotein system; Region: lipo_with_rSAM; TIGR04134 1184267004757 HEAT repeats; Region: HEAT_2; pfam13646 1184267004758 dihydroorotase; Validated; Region: PRK09060 1184267004759 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 1184267004760 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 1184267004761 active site 1184267004762 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267004763 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 1184267004764 dimer interface [polypeptide binding]; other site 1184267004765 phosphorylation site [posttranslational modification] 1184267004766 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 1184267004767 ATP binding site [chemical binding]; other site 1184267004768 Mg2+ binding site [ion binding]; other site 1184267004769 G-X-G motif; other site 1184267004770 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267004771 catalytic triad [active] 1184267004772 putative active site [active] 1184267004773 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 1184267004774 Bacitracin resistance protein BacA; Region: BacA; pfam02673 1184267004775 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1184267004776 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1184267004777 PilZ domain; Region: PilZ; pfam07238 1184267004778 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1184267004779 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 1184267004780 active site 1184267004781 metal binding site [ion binding]; metal-binding site 1184267004782 ribonuclease PH; Reviewed; Region: rph; PRK00173 1184267004783 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1184267004784 hexamer interface [polypeptide binding]; other site 1184267004785 active site 1184267004786 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 1184267004787 active site 1184267004788 dimerization interface [polypeptide binding]; other site 1184267004789 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 1184267004790 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1184267004791 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1184267004792 active site 1184267004793 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1184267004794 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 1184267004795 5S rRNA interface [nucleotide binding]; other site 1184267004796 CTC domain interface [polypeptide binding]; other site 1184267004797 L16 interface [polypeptide binding]; other site 1184267004798 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 1184267004799 putative active site [active] 1184267004800 catalytic residue [active] 1184267004801 GTP-binding protein YchF; Reviewed; Region: PRK09601 1184267004802 YchF GTPase; Region: YchF; cd01900 1184267004803 G1 box; other site 1184267004804 GTP/Mg2+ binding site [chemical binding]; other site 1184267004805 Switch I region; other site 1184267004806 G2 box; other site 1184267004807 Switch II region; other site 1184267004808 G3 box; other site 1184267004809 G4 box; other site 1184267004810 G5 box; other site 1184267004811 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 1184267004812 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1184267004813 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 1184267004814 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1184267004815 catalytic residue [active] 1184267004816 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 1184267004817 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 1184267004818 ligand binding site [chemical binding]; other site 1184267004819 flexible hinge region; other site 1184267004820 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 1184267004821 glycerol kinase; Provisional; Region: glpK; PRK00047 1184267004822 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 1184267004823 N- and C-terminal domain interface [polypeptide binding]; other site 1184267004824 active site 1184267004825 MgATP binding site [chemical binding]; other site 1184267004826 catalytic site [active] 1184267004827 metal binding site [ion binding]; metal-binding site 1184267004828 glycerol binding site [chemical binding]; other site 1184267004829 homotetramer interface [polypeptide binding]; other site 1184267004830 homodimer interface [polypeptide binding]; other site 1184267004831 FBP binding site [chemical binding]; other site 1184267004832 protein IIAGlc interface [polypeptide binding]; other site 1184267004833 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1184267004834 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like; Region: LPLAT_MGAT-like; cd07987 1184267004835 putative acyl-acceptor binding pocket; other site 1184267004836 imidazolonepropionase; Validated; Region: PRK09356 1184267004837 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 1184267004838 active site 1184267004839 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 1184267004840 catalytic core [active] 1184267004841 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1184267004842 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 1184267004843 TPP-binding site [chemical binding]; other site 1184267004844 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1184267004845 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1184267004846 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 1184267004847 E3 interaction surface; other site 1184267004848 lipoyl attachment site [posttranslational modification]; other site 1184267004849 e3 binding domain; Region: E3_binding; pfam02817 1184267004850 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1184267004851 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1184267004852 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1184267004853 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1184267004854 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1184267004855 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 1184267004856 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1184267004857 urocanate hydratase; Provisional; Region: PRK05414 1184267004858 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 1184267004859 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 1184267004860 active sites [active] 1184267004861 tetramer interface [polypeptide binding]; other site 1184267004862 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 1184267004863 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 1184267004864 substrate binding site [chemical binding]; other site 1184267004865 hexamer interface [polypeptide binding]; other site 1184267004866 metal binding site [ion binding]; metal-binding site 1184267004867 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1184267004868 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1184267004869 putative active site [active] 1184267004870 substrate binding site [chemical binding]; other site 1184267004871 putative cosubstrate binding site; other site 1184267004872 catalytic site [active] 1184267004873 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1184267004874 substrate binding site [chemical binding]; other site 1184267004875 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 1184267004876 active site 1184267004877 catalytic residues [active] 1184267004878 metal binding site [ion binding]; metal-binding site 1184267004879 Predicted permeases [General function prediction only]; Region: COG0795 1184267004880 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1184267004881 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1184267004882 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267004883 active site 1184267004884 phosphorylation site [posttranslational modification] 1184267004885 intermolecular recognition site; other site 1184267004886 dimerization interface [polypeptide binding]; other site 1184267004887 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 1184267004888 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 1184267004889 dimerization interface [polypeptide binding]; other site 1184267004890 active site 1184267004891 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1184267004892 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1184267004893 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 1184267004894 putative catalytic residue [active] 1184267004895 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 1184267004896 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 1184267004897 aconitate hydratase, mitochondrial; Region: aconitase_mito; TIGR01340 1184267004898 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 1184267004899 substrate binding site [chemical binding]; other site 1184267004900 ligand binding site [chemical binding]; other site 1184267004901 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 1184267004902 substrate binding site [chemical binding]; other site 1184267004903 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267004904 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267004905 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 1184267004906 dimerization interface [polypeptide binding]; other site 1184267004907 DNA topoisomerase VI subunit A; Provisional; Region: PRK04342 1184267004908 Type IIB DNA topoisomerase; Region: TP6A_N; pfam04406 1184267004909 TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI)...; Region: TOPRIM_TopoIIB_SPO; cd00223 1184267004910 active site 1184267004911 metal binding site [ion binding]; metal-binding site 1184267004912 interdomain interaction site; other site 1184267004913 DNA topoisomerase VI subunit B; Validated; Region: PRK04184 1184267004914 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 1184267004915 ATP binding site [chemical binding]; other site 1184267004916 Mg2+ binding site [ion binding]; other site 1184267004917 G-X-G motif; other site 1184267004918 TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB...; Region: TopoIIB_Trans; cd00823 1184267004919 anchoring element; other site 1184267004920 dimer interface [polypeptide binding]; other site 1184267004921 ATP binding site [chemical binding]; other site 1184267004922 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1184267004923 EamA-like transporter family; Region: EamA; pfam00892 1184267004924 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 1184267004925 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 1184267004926 active site 1184267004927 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1184267004928 Sulfatase; Region: Sulfatase; cl17466 1184267004929 BolA-like protein; Region: BolA; pfam01722 1184267004930 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 1184267004931 putative GSH binding site [chemical binding]; other site 1184267004932 catalytic residues [active] 1184267004933 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1184267004934 FAD binding domain; Region: FAD_binding_4; pfam01565 1184267004935 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 1184267004936 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 1184267004937 ligand binding site [chemical binding]; other site 1184267004938 NAD binding site [chemical binding]; other site 1184267004939 tetramer interface [polypeptide binding]; other site 1184267004940 catalytic site [active] 1184267004941 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 1184267004942 L-serine binding site [chemical binding]; other site 1184267004943 ACT domain interface; other site 1184267004944 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1184267004945 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267004946 active site 1184267004947 phosphorylation site [posttranslational modification] 1184267004948 intermolecular recognition site; other site 1184267004949 dimerization interface [polypeptide binding]; other site 1184267004950 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 1184267004951 Walker A motif; other site 1184267004952 ATP binding site [chemical binding]; other site 1184267004953 Walker B motif; other site 1184267004954 arginine finger; other site 1184267004955 Cytidylyltransferase family; Region: CTP_transf_1; cl17467 1184267004956 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1184267004957 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1184267004958 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1184267004959 putative acyl-acceptor binding pocket; other site 1184267004960 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 1184267004961 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 1184267004962 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 1184267004963 active site 1184267004964 catalytic residues [active] 1184267004965 DNA binding site [nucleotide binding] 1184267004966 Int/Topo IB signature motif; other site 1184267004967 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1184267004968 active site 1184267004969 NTP binding site [chemical binding]; other site 1184267004970 metal binding triad [ion binding]; metal-binding site 1184267004971 antibiotic binding site [chemical binding]; other site 1184267004972 HEPN domain; Region: HEPN; pfam05168 1184267004973 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 1184267004974 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 1184267004975 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 1184267004976 Replication initiation factor; Region: Rep_trans; pfam02486 1184267004977 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 1184267004978 Helix-turn-helix domain; Region: HTH_18; pfam12833 1184267004979 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 1184267004980 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 1184267004981 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 1184267004982 NodB motif; other site 1184267004983 active site 1184267004984 catalytic site [active] 1184267004985 metal binding site [ion binding]; metal-binding site 1184267004986 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 1184267004987 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1184267004988 metal-binding site [ion binding] 1184267004989 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1184267004990 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1184267004991 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 1184267004992 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 1184267004993 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1184267004994 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1184267004995 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1184267004996 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 1184267004997 Predicted flavoprotein [General function prediction only]; Region: COG0431 1184267004998 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 1184267004999 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 1184267005000 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 1184267005001 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 1184267005002 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 1184267005003 active site 1184267005004 Zn binding site [ion binding]; other site 1184267005005 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 1184267005006 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 1184267005007 inhibitor-cofactor binding pocket; inhibition site 1184267005008 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267005009 catalytic residue [active] 1184267005010 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1184267005011 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 1184267005012 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 1184267005013 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 1184267005014 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 1184267005015 homodimer interface [polypeptide binding]; other site 1184267005016 substrate-cofactor binding pocket; other site 1184267005017 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267005018 catalytic residue [active] 1184267005019 TIGR03546 family protein; Region: TIGR03546 1184267005020 TIGR03545 family protein; Region: TIGR03545 1184267005021 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1184267005022 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 1184267005023 catalytic residues [active] 1184267005024 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 1184267005025 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1184267005026 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1184267005027 alphaNTD homodimer interface [polypeptide binding]; other site 1184267005028 alphaNTD - beta interaction site [polypeptide binding]; other site 1184267005029 alphaNTD - beta' interaction site [polypeptide binding]; other site 1184267005030 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1184267005031 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1184267005032 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1184267005033 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 1184267005034 RNA binding surface [nucleotide binding]; other site 1184267005035 30S ribosomal protein S11; Validated; Region: PRK05309 1184267005036 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 1184267005037 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1184267005038 adenylate kinase; Reviewed; Region: adk; PRK00279 1184267005039 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 1184267005040 AMP-binding site [chemical binding]; other site 1184267005041 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1184267005042 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1184267005043 SecY translocase; Region: SecY; pfam00344 1184267005044 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1184267005045 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 1184267005046 23S rRNA binding site [nucleotide binding]; other site 1184267005047 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1184267005048 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1184267005049 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1184267005050 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 1184267005051 23S rRNA interface [nucleotide binding]; other site 1184267005052 L21e interface [polypeptide binding]; other site 1184267005053 5S rRNA interface [nucleotide binding]; other site 1184267005054 L27 interface [polypeptide binding]; other site 1184267005055 L5 interface [polypeptide binding]; other site 1184267005056 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1184267005057 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1184267005058 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1184267005059 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1184267005060 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1184267005061 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1184267005062 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1184267005063 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1184267005064 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1184267005065 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1184267005066 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 1184267005067 putative translocon interaction site; other site 1184267005068 23S rRNA interface [nucleotide binding]; other site 1184267005069 signal recognition particle (SRP54) interaction site; other site 1184267005070 L23 interface [polypeptide binding]; other site 1184267005071 trigger factor interaction site; other site 1184267005072 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 1184267005073 23S rRNA interface [nucleotide binding]; other site 1184267005074 5S rRNA interface [nucleotide binding]; other site 1184267005075 putative antibiotic binding site [chemical binding]; other site 1184267005076 L25 interface [polypeptide binding]; other site 1184267005077 L27 interface [polypeptide binding]; other site 1184267005078 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1184267005079 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 1184267005080 G-X-X-G motif; other site 1184267005081 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1184267005082 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 1184267005083 putative translocon binding site; other site 1184267005084 protein-rRNA interface [nucleotide binding]; other site 1184267005085 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1184267005086 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1184267005087 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1184267005088 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1184267005089 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1184267005090 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1184267005091 50S ribosomal protein L3, bacterial; Region: L3_bact; TIGR03625 1184267005092 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1184267005093 elongation factor G; Reviewed; Region: PRK00007 1184267005094 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1184267005095 G1 box; other site 1184267005096 putative GEF interaction site [polypeptide binding]; other site 1184267005097 GTP/Mg2+ binding site [chemical binding]; other site 1184267005098 Switch I region; other site 1184267005099 G2 box; other site 1184267005100 G3 box; other site 1184267005101 Switch II region; other site 1184267005102 G4 box; other site 1184267005103 G5 box; other site 1184267005104 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 1184267005105 Elongation factor G, domain IV; Region: EFG_IV; smart00889 1184267005106 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 1184267005107 30S ribosomal protein S7; Validated; Region: PRK05302 1184267005108 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 1184267005109 S17 interaction site [polypeptide binding]; other site 1184267005110 S8 interaction site; other site 1184267005111 16S rRNA interaction site [nucleotide binding]; other site 1184267005112 streptomycin interaction site [chemical binding]; other site 1184267005113 23S rRNA interaction site [nucleotide binding]; other site 1184267005114 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1184267005115 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1184267005116 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1184267005117 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1184267005118 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1184267005119 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1184267005120 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1184267005121 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1184267005122 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1184267005123 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1184267005124 DNA binding site [nucleotide binding] 1184267005125 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1184267005126 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1184267005127 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 1184267005128 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1184267005129 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 1184267005130 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1184267005131 RPB12 interaction site [polypeptide binding]; other site 1184267005132 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 1184267005133 RPB3 interaction site [polypeptide binding]; other site 1184267005134 RPB1 interaction site [polypeptide binding]; other site 1184267005135 RPB11 interaction site [polypeptide binding]; other site 1184267005136 RPB10 interaction site [polypeptide binding]; other site 1184267005137 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 1184267005138 core dimer interface [polypeptide binding]; other site 1184267005139 peripheral dimer interface [polypeptide binding]; other site 1184267005140 L10 interface [polypeptide binding]; other site 1184267005141 L11 interface [polypeptide binding]; other site 1184267005142 putative EF-Tu interaction site [polypeptide binding]; other site 1184267005143 putative EF-G interaction site [polypeptide binding]; other site 1184267005144 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 1184267005145 23S rRNA interface [nucleotide binding]; other site 1184267005146 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1184267005147 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 1184267005148 mRNA/rRNA interface [nucleotide binding]; other site 1184267005149 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1184267005150 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 1184267005151 23S rRNA interface [nucleotide binding]; other site 1184267005152 L7/L12 interface [polypeptide binding]; other site 1184267005153 putative thiostrepton binding site; other site 1184267005154 L25 interface [polypeptide binding]; other site 1184267005155 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1184267005156 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1184267005157 putative homodimer interface [polypeptide binding]; other site 1184267005158 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1184267005159 heterodimer interface [polypeptide binding]; other site 1184267005160 homodimer interface [polypeptide binding]; other site 1184267005161 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 1184267005162 elongation factor Tu; Reviewed; Region: PRK00049 1184267005163 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1184267005164 G1 box; other site 1184267005165 GEF interaction site [polypeptide binding]; other site 1184267005166 GTP/Mg2+ binding site [chemical binding]; other site 1184267005167 Switch I region; other site 1184267005168 G2 box; other site 1184267005169 G3 box; other site 1184267005170 Switch II region; other site 1184267005171 G4 box; other site 1184267005172 G5 box; other site 1184267005173 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 1184267005174 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 1184267005175 Antibiotic Binding Site [chemical binding]; other site 1184267005176 AAA domain; Region: AAA_17; pfam13207 1184267005177 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 1184267005178 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 1184267005179 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 1184267005180 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1184267005181 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 1184267005182 active site 1184267005183 dimer interface [polypeptide binding]; other site 1184267005184 prolyl-tRNA synthetase; Provisional; Region: PRK09194 1184267005185 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 1184267005186 dimer interface [polypeptide binding]; other site 1184267005187 motif 1; other site 1184267005188 active site 1184267005189 motif 2; other site 1184267005190 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 1184267005191 putative deacylase active site [active] 1184267005192 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 1184267005193 active site 1184267005194 motif 3; other site 1184267005195 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 1184267005196 anticodon binding site; other site 1184267005197 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1184267005198 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267005199 active site 1184267005200 phosphorylation site [posttranslational modification] 1184267005201 intermolecular recognition site; other site 1184267005202 dimerization interface [polypeptide binding]; other site 1184267005203 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 1184267005204 Walker A motif; other site 1184267005205 ATP binding site [chemical binding]; other site 1184267005206 Walker B motif; other site 1184267005207 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 1184267005208 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 1184267005209 dimerization interface [polypeptide binding]; other site 1184267005210 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 1184267005211 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267005212 putative active site [active] 1184267005213 heme pocket [chemical binding]; other site 1184267005214 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 1184267005215 dimer interface [polypeptide binding]; other site 1184267005216 phosphorylation site [posttranslational modification] 1184267005217 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 1184267005218 ATP binding site [chemical binding]; other site 1184267005219 Mg2+ binding site [ion binding]; other site 1184267005220 G-X-G motif; other site 1184267005221 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 1184267005222 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 1184267005223 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1184267005224 Clp amino terminal domain; Region: Clp_N; pfam02861 1184267005225 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 1184267005226 Walker A motif; other site 1184267005227 ATP binding site [chemical binding]; other site 1184267005228 Walker B motif; other site 1184267005229 arginine finger; other site 1184267005230 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 1184267005231 Walker A motif; other site 1184267005232 ATP binding site [chemical binding]; other site 1184267005233 Walker B motif; other site 1184267005234 arginine finger; other site 1184267005235 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1184267005236 flagellin; Provisional; Region: PRK12802 1184267005237 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1184267005238 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1184267005239 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 1184267005240 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 1184267005241 Walker A motif; other site 1184267005242 ATP binding site [chemical binding]; other site 1184267005243 Walker B motif; other site 1184267005244 arginine finger; other site 1184267005245 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267005246 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1184267005247 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 1184267005248 active site 1184267005249 DNA binding site [nucleotide binding] 1184267005250 Int/Topo IB signature motif; other site 1184267005251 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1184267005252 Protein export membrane protein; Region: SecD_SecF; cl14618 1184267005253 Recombination protein O N terminal; Region: RecO_N; pfam11967 1184267005254 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 1184267005255 4Fe-4S binding domain; Region: Fer4; pfam00037 1184267005256 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 1184267005257 catalytic loop [active] 1184267005258 iron binding site [ion binding]; other site 1184267005259 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1184267005260 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 1184267005261 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 1184267005262 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 1184267005263 SLBB domain; Region: SLBB; pfam10531 1184267005264 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 1184267005265 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 1184267005266 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 1184267005267 putative dimer interface [polypeptide binding]; other site 1184267005268 [2Fe-2S] cluster binding site [ion binding]; other site 1184267005269 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1184267005270 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1184267005271 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 1184267005272 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1184267005273 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1184267005274 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267005275 catalytic triad [active] 1184267005276 putative active site [active] 1184267005277 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 1184267005278 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 1184267005279 PilZ domain; Region: PilZ; pfam07238 1184267005280 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 1184267005281 nucleotide binding site [chemical binding]; other site 1184267005282 putative NEF/HSP70 interaction site [polypeptide binding]; other site 1184267005283 SBD interface [polypeptide binding]; other site 1184267005284 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 1184267005285 active site 1184267005286 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 1184267005287 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 1184267005288 dimer interface [polypeptide binding]; other site 1184267005289 conserved gate region; other site 1184267005290 ABC-ATPase subunit interface; other site 1184267005291 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 1184267005292 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 1184267005293 Walker A/P-loop; other site 1184267005294 ATP binding site [chemical binding]; other site 1184267005295 Q-loop/lid; other site 1184267005296 ABC transporter signature motif; other site 1184267005297 Walker B; other site 1184267005298 D-loop; other site 1184267005299 H-loop/switch region; other site 1184267005300 phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein; Region: 3A0109s03R; TIGR01098 1184267005301 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 1184267005302 substrate binding pocket [chemical binding]; other site 1184267005303 membrane-bound complex binding site; other site 1184267005304 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 1184267005305 HAD superfamily, subfamily IIIB (Acid phosphatase); Region: Acid_phosphat_B; cl17236 1184267005306 S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase; cl00304 1184267005307 active site 1184267005308 homodimer interface [polypeptide binding]; other site 1184267005309 SAM binding site [chemical binding]; other site 1184267005310 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 1184267005311 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 1184267005312 ATP binding site [chemical binding]; other site 1184267005313 putative Mg++ binding site [ion binding]; other site 1184267005314 nucleotide binding region [chemical binding]; other site 1184267005315 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1184267005316 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 1184267005317 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 1184267005318 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 1184267005319 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1184267005320 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 1184267005321 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 1184267005322 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 1184267005323 serine O-acetyltransferase; Region: cysE; TIGR01172 1184267005324 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 1184267005325 trimer interface [polypeptide binding]; other site 1184267005326 active site 1184267005327 substrate binding site [chemical binding]; other site 1184267005328 CoA binding site [chemical binding]; other site 1184267005329 YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is...; Region: YhaM_OBF_like; cd04492 1184267005330 generic binding surface II; other site 1184267005331 Predicted HD-superfamily hydrolase [General function prediction only]; Region: COG3481 1184267005332 generic binding surface I; other site 1184267005333 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267005334 Zn2+ binding site [ion binding]; other site 1184267005335 Mg2+ binding site [ion binding]; other site 1184267005336 mce related protein; Region: MCE; pfam02470 1184267005337 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1184267005338 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1184267005339 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 1184267005340 Walker A/P-loop; other site 1184267005341 ATP binding site [chemical binding]; other site 1184267005342 Q-loop/lid; other site 1184267005343 ABC transporter signature motif; other site 1184267005344 Walker B; other site 1184267005345 D-loop; other site 1184267005346 H-loop/switch region; other site 1184267005347 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1184267005348 Permease; Region: Permease; pfam02405 1184267005349 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1184267005350 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1184267005351 active site 1184267005352 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1184267005353 dimer interface [polypeptide binding]; other site 1184267005354 substrate binding site [chemical binding]; other site 1184267005355 catalytic residues [active] 1184267005356 cheY-homologous receiver domain; Region: REC; smart00448 1184267005357 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1184267005358 metal binding site [ion binding]; metal-binding site 1184267005359 active site 1184267005360 I-site; other site 1184267005361 L-aspartate oxidase; Provisional; Region: PRK09077 1184267005362 L-aspartate oxidase; Provisional; Region: PRK06175 1184267005363 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1184267005364 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 1184267005365 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1184267005366 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1184267005367 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1184267005368 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 1184267005369 putative dimer interface [polypeptide binding]; other site 1184267005370 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1184267005371 RNA/DNA hybrid binding site [nucleotide binding]; other site 1184267005372 active site 1184267005373 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 1184267005374 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 1184267005375 active site 1184267005376 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1184267005377 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267005378 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267005379 Walker A/P-loop; other site 1184267005380 Walker A/P-loop; other site 1184267005381 ATP binding site [chemical binding]; other site 1184267005382 ATP binding site [chemical binding]; other site 1184267005383 Q-loop/lid; other site 1184267005384 ABC transporter signature motif; other site 1184267005385 Walker B; other site 1184267005386 D-loop; other site 1184267005387 H-loop/switch region; other site 1184267005388 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 1184267005389 Family description; Region: UvrD_C_2; pfam13538 1184267005390 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 1184267005391 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 1184267005392 F plasmid transfer operon, TraF, protein; Region: TraF_2; pfam13729 1184267005393 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 1184267005394 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 1184267005395 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1184267005396 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 1184267005397 CoA-binding site [chemical binding]; other site 1184267005398 ATP-binding [chemical binding]; other site 1184267005399 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1184267005400 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 1184267005401 active site 1184267005402 ATP binding site [chemical binding]; other site 1184267005403 substrate binding site [chemical binding]; other site 1184267005404 activation loop (A-loop); other site 1184267005405 PEGA domain; Region: PEGA; pfam08308 1184267005406 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 1184267005407 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 1184267005408 acyl-activating enzyme (AAE) consensus motif; other site 1184267005409 putative AMP binding site [chemical binding]; other site 1184267005410 putative active site [active] 1184267005411 putative CoA binding site [chemical binding]; other site 1184267005412 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 1184267005413 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 1184267005414 active site 1184267005415 Zn binding site [ion binding]; other site 1184267005416 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 1184267005417 ATP-NAD kinase; Region: NAD_kinase; pfam01513 1184267005418 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1184267005419 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1184267005420 Walker A/P-loop; other site 1184267005421 ATP binding site [chemical binding]; other site 1184267005422 Q-loop/lid; other site 1184267005423 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1184267005424 ABC transporter signature motif; other site 1184267005425 Walker B; other site 1184267005426 D-loop; other site 1184267005427 H-loop/switch region; other site 1184267005428 Integral membrane protein TerC family; Region: TerC; cl10468 1184267005429 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267005430 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267005431 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 1184267005432 dimerization interface [polypeptide binding]; other site 1184267005433 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 1184267005434 putative active site [active] 1184267005435 putative metal binding site [ion binding]; other site 1184267005436 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 1184267005437 cell division protein FtsZ; Validated; Region: PRK09330 1184267005438 nucleotide binding site [chemical binding]; other site 1184267005439 SulA interaction site; other site 1184267005440 cell division protein FtsA; Region: ftsA; TIGR01174 1184267005441 Cell division protein FtsA; Region: FtsA; smart00842 1184267005442 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1184267005443 Cell division protein FtsA; Region: FtsA; pfam14450 1184267005444 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1184267005445 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1184267005446 FAD binding domain; Region: FAD_binding_4; pfam01565 1184267005447 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1184267005448 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1184267005449 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1184267005450 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1184267005451 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1184267005452 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1184267005453 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 1184267005454 active site 1184267005455 homodimer interface [polypeptide binding]; other site 1184267005456 cell division protein FtsW; Region: ftsW; TIGR02614 1184267005457 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 1184267005458 UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]; Region: MurD; COG0771 1184267005459 NAD binding site [chemical binding]; other site 1184267005460 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1184267005461 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1184267005462 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1184267005463 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 1184267005464 Mg++ binding site [ion binding]; other site 1184267005465 putative catalytic motif [active] 1184267005466 putative substrate binding site [chemical binding]; other site 1184267005467 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 1184267005468 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 1184267005469 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1184267005470 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1184267005471 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1184267005472 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1184267005473 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1184267005474 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1184267005475 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1184267005476 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1184267005477 Predicted esterase [General function prediction only]; Region: COG0400 1184267005478 Serine hydrolase (FSH1); Region: FSH1; pfam03959 1184267005479 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4586 1184267005480 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267005481 Walker A/P-loop; other site 1184267005482 ATP binding site [chemical binding]; other site 1184267005483 Q-loop/lid; other site 1184267005484 ABC transporter signature motif; other site 1184267005485 Walker B; other site 1184267005486 D-loop; other site 1184267005487 H-loop/switch region; other site 1184267005488 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4587 1184267005489 ABC-2 family transporter protein; Region: ABC2_membrane_6; cl01496 1184267005490 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1184267005491 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1184267005492 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1184267005493 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 1184267005494 MraW methylase family; Region: Methyltransf_5; cl17771 1184267005495 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1184267005496 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1184267005497 active site 1184267005498 thymidylate synthase; Reviewed; Region: thyA; PRK01827 1184267005499 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 1184267005500 dimerization interface [polypeptide binding]; other site 1184267005501 active site 1184267005502 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1184267005503 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 1184267005504 folate binding site [chemical binding]; other site 1184267005505 NADP+ binding site [chemical binding]; other site 1184267005506 PilZ domain; Region: PilZ; pfam07238 1184267005507 Peptidase M14 Carboxypeptidase T subfamily; Region: M14_CPT; cd03859 1184267005508 putative active site [active] 1184267005509 Zn binding site [ion binding]; other site 1184267005510 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 1184267005511 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1184267005512 catalytic residue [active] 1184267005513 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 1184267005514 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 1184267005515 Signal peptidase (SPase) II; Region: Peptidase_A8; pfam01252 1184267005516 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 1184267005517 active site 1184267005518 catalytic site [active] 1184267005519 substrate binding site [chemical binding]; other site 1184267005520 WYL domain; Region: WYL; cl14852 1184267005521 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 1184267005522 flagellar motor protein MotA; Validated; Region: PRK09110 1184267005523 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 1184267005524 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 1184267005525 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 1184267005526 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 1184267005527 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1184267005528 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1184267005529 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 1184267005530 RNA binding surface [nucleotide binding]; other site 1184267005531 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 1184267005532 active site 1184267005533 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 1184267005534 cyclase homology domain; Region: CHD; cd07302 1184267005535 nucleotidyl binding site; other site 1184267005536 metal binding site [ion binding]; metal-binding site 1184267005537 dimer interface [polypeptide binding]; other site 1184267005538 Methyltransferase domain; Region: Methyltransf_25; pfam13649 1184267005539 oxaloacetate decarboxylase alpha subunit; Region: oadA; TIGR01108 1184267005540 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 1184267005541 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 1184267005542 S-adenosylmethionine binding site [chemical binding]; other site 1184267005543 RNA methyltransferase, RsmE family; Region: TIGR00046 1184267005544 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 1184267005545 RDD family; Region: RDD; pfam06271 1184267005546 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 1184267005547 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 1184267005548 active site 1184267005549 nucleotide binding site [chemical binding]; other site 1184267005550 HIGH motif; other site 1184267005551 KMSKS motif; other site 1184267005552 Flagellin N-methylase; Region: FliB; pfam03692 1184267005553 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2933 1184267005554 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1184267005555 PilZ domain; Region: PilZ; pfam07238 1184267005556 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 1184267005557 SmpB-tmRNA interface; other site 1184267005558 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1184267005559 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 1184267005560 S-adenosylmethionine binding site [chemical binding]; other site 1184267005561 tRNA threonylcarbamoyl adenosine modification protein YgjD; Region: T6A_YgjD; TIGR03723 1184267005562 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 1184267005563 RPAP1-like, N-terminal; Region: RPAP1_N; pfam08621 1184267005564 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1184267005565 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 1184267005566 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 1184267005567 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1184267005568 ligand binding site [chemical binding]; other site 1184267005569 Peptidase MA superfamily; Region: Peptidase_MA_2; pfam13485 1184267005570 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 1184267005571 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 1184267005572 aspartate aminotransferase; Provisional; Region: PRK05764 1184267005573 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 1184267005574 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267005575 homodimer interface [polypeptide binding]; other site 1184267005576 catalytic residue [active] 1184267005577 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 1184267005578 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 1184267005579 active site 1184267005580 (T/H)XGH motif; other site 1184267005581 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1184267005582 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 1184267005583 S-adenosylmethionine binding site [chemical binding]; other site 1184267005584 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267005585 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267005586 active site 1184267005587 phosphorylation site [posttranslational modification] 1184267005588 intermolecular recognition site; other site 1184267005589 dimerization interface [polypeptide binding]; other site 1184267005590 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 1184267005591 dimer interface [polypeptide binding]; other site 1184267005592 phosphorylation site [posttranslational modification] 1184267005593 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 1184267005594 ATP binding site [chemical binding]; other site 1184267005595 Mg2+ binding site [ion binding]; other site 1184267005596 G-X-G motif; other site 1184267005597 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 1184267005598 TPR motif; other site 1184267005599 binding surface 1184267005600 Flagellar protein FliS; Region: FliS; cl00654 1184267005601 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 1184267005602 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 1184267005603 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 1184267005604 flagellin; Provisional; Region: PRK12802 1184267005605 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1184267005606 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1184267005607 flagellin; Provisional; Region: PRK12802 1184267005608 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1184267005609 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1184267005610 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1184267005611 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267005612 Walker A/P-loop; other site 1184267005613 ATP binding site [chemical binding]; other site 1184267005614 Q-loop/lid; other site 1184267005615 ABC transporter signature motif; other site 1184267005616 Walker B; other site 1184267005617 D-loop; other site 1184267005618 H-loop/switch region; other site 1184267005619 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 1184267005620 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 1184267005621 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1184267005622 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1184267005623 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1184267005624 minor groove reading motif; other site 1184267005625 helix-hairpin-helix signature motif; other site 1184267005626 substrate binding pocket [chemical binding]; other site 1184267005627 active site 1184267005628 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1184267005629 4Fe-4S single cluster domain; Region: Fer4_13; pfam13370 1184267005630 Predicted acetyltransferase involved in intracellular survival and related acetyltransferases [General function prediction only]; Region: Eis; COG4552 1184267005631 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1184267005632 Coenzyme A binding pocket [chemical binding]; other site 1184267005633 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 1184267005634 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1184267005635 D-ala D-ala ligase C-terminus; Region: Dala_Dala_lig_C; pfam07478 1184267005636 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1184267005637 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1184267005638 NAD(P) binding site [chemical binding]; other site 1184267005639 catalytic residues [active] 1184267005640 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 1184267005641 nucleotide binding site/active site [active] 1184267005642 HIT family signature motif; other site 1184267005643 catalytic residue [active] 1184267005644 Late embryogenesis abundant protein; Region: LEA_2; cl12118 1184267005645 Late embryogenesis abundant protein; Region: LEA_2; pfam03168 1184267005646 Bacillus subtilis (Bs) citrate synthase (CS)-II_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). 2MCS catalyzes the...; Region: BSuCS-II_like; cd06110 1184267005647 dimer interface [polypeptide binding]; other site 1184267005648 Citrate synthase; Region: Citrate_synt; pfam00285 1184267005649 active site 1184267005650 citrylCoA binding site [chemical binding]; other site 1184267005651 oxalacetate/citrate binding site [chemical binding]; other site 1184267005652 coenzyme A binding site [chemical binding]; other site 1184267005653 catalytic triad [active] 1184267005654 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 1184267005655 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 1184267005656 S-adenosylmethionine binding site [chemical binding]; other site 1184267005657 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]; Region: MenA; cl17224 1184267005658 UbiA prenyltransferase family; Region: UbiA; pfam01040 1184267005659 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1184267005660 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1184267005661 substrate binding pocket [chemical binding]; other site 1184267005662 chain length determination region; other site 1184267005663 substrate-Mg2+ binding site; other site 1184267005664 catalytic residues [active] 1184267005665 aspartate-rich region 1; other site 1184267005666 active site lid residues [active] 1184267005667 aspartate-rich region 2; other site 1184267005668 Flagellin N-methylase; Region: FliB; pfam03692 1184267005669 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 1184267005670 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267005671 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 1184267005672 ATP binding site [chemical binding]; other site 1184267005673 Mg2+ binding site [ion binding]; other site 1184267005674 G-X-G motif; other site 1184267005675 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 1184267005676 Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]; Region: AslB; COG0641 1184267005677 FeS/SAM binding site; other site 1184267005678 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 1184267005679 CHASE2 domain; Region: CHASE2; pfam05226 1184267005680 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 1184267005681 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267005682 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 1184267005683 dimer interface [polypeptide binding]; other site 1184267005684 phosphorylation site [posttranslational modification] 1184267005685 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 1184267005686 ATP binding site [chemical binding]; other site 1184267005687 Mg2+ binding site [ion binding]; other site 1184267005688 G-X-G motif; other site 1184267005689 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1184267005690 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267005691 active site 1184267005692 phosphorylation site [posttranslational modification] 1184267005693 intermolecular recognition site; other site 1184267005694 dimerization interface [polypeptide binding]; other site 1184267005695 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 1184267005696 Walker A motif; other site 1184267005697 ATP binding site [chemical binding]; other site 1184267005698 Walker B motif; other site 1184267005699 arginine finger; other site 1184267005700 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267005701 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 1184267005702 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1184267005703 active site 1184267005704 HIGH motif; other site 1184267005705 nucleotide binding site [chemical binding]; other site 1184267005706 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1184267005707 active site 1184267005708 KMSKS motif; other site 1184267005709 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 1184267005710 tRNA binding surface [nucleotide binding]; other site 1184267005711 anticodon binding site; other site 1184267005712 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1184267005713 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1184267005714 Prolipoprotein diacylglyceryl transferase; Region: LGT; pfam01790 1184267005715 Domain of unknown function (DUF329); Region: DUF329; pfam03884 1184267005716 Amino acid permease; Region: AA_permease_2; pfam13520 1184267005717 K+ potassium transporter; Region: K_trans; cl15781 1184267005718 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 1184267005719 IHF - DNA interface [nucleotide binding]; other site 1184267005720 IHF dimer interface [polypeptide binding]; other site 1184267005721 6-phosphofructokinase; Provisional; Region: PRK03202 1184267005722 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 1184267005723 active site 1184267005724 ADP/pyrophosphate binding site [chemical binding]; other site 1184267005725 dimerization interface [polypeptide binding]; other site 1184267005726 allosteric effector site; other site 1184267005727 fructose-1,6-bisphosphate binding site; other site 1184267005728 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 1184267005729 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_12; cd06347 1184267005730 putative ligand binding site [chemical binding]; other site 1184267005731 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 1184267005732 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 1184267005733 TM-ABC transporter signature motif; other site 1184267005734 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 1184267005735 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 1184267005736 TM-ABC transporter signature motif; other site 1184267005737 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 1184267005738 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 1184267005739 Walker A/P-loop; other site 1184267005740 ATP binding site [chemical binding]; other site 1184267005741 Q-loop/lid; other site 1184267005742 ABC transporter signature motif; other site 1184267005743 Walker B; other site 1184267005744 D-loop; other site 1184267005745 H-loop/switch region; other site 1184267005746 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 1184267005747 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 1184267005748 Walker A/P-loop; other site 1184267005749 ATP binding site [chemical binding]; other site 1184267005750 Q-loop/lid; other site 1184267005751 ABC transporter signature motif; other site 1184267005752 Walker B; other site 1184267005753 D-loop; other site 1184267005754 H-loop/switch region; other site 1184267005755 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 1184267005756 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 1184267005757 Transglutaminase/protease-like homologues; Region: TGc; smart00460 1184267005758 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 1184267005759 TPR motif; other site 1184267005760 TPR repeat; Region: TPR_11; pfam13414 1184267005761 binding surface 1184267005762 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 1184267005763 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 1184267005764 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 1184267005765 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 1184267005766 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1184267005767 Walker A/P-loop; other site 1184267005768 ATP binding site [chemical binding]; other site 1184267005769 Q-loop/lid; other site 1184267005770 ABC transporter signature motif; other site 1184267005771 Walker B; other site 1184267005772 D-loop; other site 1184267005773 H-loop/switch region; other site 1184267005774 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1184267005775 FtsX-like permease family; Region: FtsX; pfam02687 1184267005776 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1184267005777 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1184267005778 HlyD family secretion protein; Region: HlyD_3; pfam13437 1184267005779 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 1184267005780 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 1184267005781 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1184267005782 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 1184267005783 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1184267005784 Protein of unknown function (DUF3766); Region: DUF3766; cl11797 1184267005785 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 1184267005786 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 1184267005787 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 1184267005788 Flagellar hook-length control protein FliK; Region: Flg_hook; cl17777 1184267005789 Uncharacterized conserved protein [Function unknown]; Region: COG3334 1184267005790 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 1184267005791 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 1184267005792 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 1184267005793 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 1184267005794 Walker A motif/ATP binding site; other site 1184267005795 Walker B motif; other site 1184267005796 Flagellar assembly protein FliH; Region: FliH; pfam02108 1184267005797 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 1184267005798 MgtE intracellular N domain; Region: MgtE_N; cl15244 1184267005799 FliG C-terminal domain; Region: FliG_C; pfam01706 1184267005800 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 1184267005801 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 1184267005802 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 1184267005803 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 1184267005804 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 1184267005805 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1184267005806 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 1184267005807 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 1184267005808 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 1184267005809 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267005810 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1184267005811 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1184267005812 Permease; Region: Permease; pfam02405 1184267005813 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1184267005814 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 1184267005815 Walker A/P-loop; other site 1184267005816 ATP binding site [chemical binding]; other site 1184267005817 Q-loop/lid; other site 1184267005818 ABC transporter signature motif; other site 1184267005819 Walker B; other site 1184267005820 D-loop; other site 1184267005821 H-loop/switch region; other site 1184267005822 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1184267005823 mce related protein; Region: MCE; pfam02470 1184267005824 Protein of unknown function (DUF721); Region: DUF721; pfam05258 1184267005825 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 1184267005826 Glucose inhibited division protein A; Region: GIDA; pfam01134 1184267005827 PilZ domain; Region: PilZ; pfam07238 1184267005828 thymidine kinase; Provisional; Region: PRK04296 1184267005829 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 1184267005830 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1184267005831 catalytic residue [active] 1184267005832 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 1184267005833 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 1184267005834 glutaminase active site [active] 1184267005835 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 1184267005836 dimer interface [polypeptide binding]; other site 1184267005837 active site 1184267005838 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 1184267005839 dimer interface [polypeptide binding]; other site 1184267005840 active site 1184267005841 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 1184267005842 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1184267005843 Substrate binding site; other site 1184267005844 Mg++ binding site; other site 1184267005845 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 1184267005846 active site 1184267005847 substrate binding site [chemical binding]; other site 1184267005848 CoA binding site [chemical binding]; other site 1184267005849 HAD superfamily (subfamily IA) hydrolase, TIGR02253; Region: CTE7 1184267005850 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; cl17915 1184267005851 motif II; other site 1184267005852 NurA domain; Region: NurA; cl09134 1184267005853 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 1184267005854 dimer interface [polypeptide binding]; other site 1184267005855 phosphorylation site [posttranslational modification] 1184267005856 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1184267005857 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267005858 active site 1184267005859 phosphorylation site [posttranslational modification] 1184267005860 intermolecular recognition site; other site 1184267005861 dimerization interface [polypeptide binding]; other site 1184267005862 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 1184267005863 Walker A motif; other site 1184267005864 ATP binding site [chemical binding]; other site 1184267005865 Walker B motif; other site 1184267005866 arginine finger; other site 1184267005867 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1184267005868 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 1184267005869 active site 1184267005870 Zn binding site [ion binding]; other site 1184267005871 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 1184267005872 Arginase family; Region: Arginase; cd09989 1184267005873 active site 1184267005874 Mn binding site [ion binding]; other site 1184267005875 oligomer interface [polypeptide binding]; other site 1184267005876 Glutamine amidotransferase class-I; Region: GATase; pfam00117 1184267005877 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 1184267005878 glutamine binding [chemical binding]; other site 1184267005879 catalytic triad [active] 1184267005880 aminodeoxychorismate synthase, component I, clade 2; Region: PabB-clade2; TIGR01824 1184267005881 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 1184267005882 Aminotransferase class IV; Region: Aminotran_4; pfam01063 1184267005883 substrate-cofactor binding pocket; other site 1184267005884 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1184267005885 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1184267005886 putative acyl-acceptor binding pocket; other site 1184267005887 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1184267005888 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1184267005889 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 1184267005890 FtsX-like permease family; Region: FtsX; pfam02687 1184267005891 FtsX-like permease family; Region: FtsX; pfam02687 1184267005892 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1184267005893 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1184267005894 Walker A/P-loop; other site 1184267005895 ATP binding site [chemical binding]; other site 1184267005896 Q-loop/lid; other site 1184267005897 ABC transporter signature motif; other site 1184267005898 Walker B; other site 1184267005899 D-loop; other site 1184267005900 H-loop/switch region; other site 1184267005901 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 1184267005902 active site 1184267005903 catalytic triad [active] 1184267005904 oxyanion hole [active] 1184267005905 switch loop; other site 1184267005906 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 1184267005907 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 1184267005908 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1184267005909 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 1184267005910 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 1184267005911 active site 1184267005912 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1184267005913 Coenzyme A binding pocket [chemical binding]; other site 1184267005914 Protein of unknown function (DUF1365); Region: DUF1365; cl17838 1184267005915 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 1184267005916 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1184267005917 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 1184267005918 active site 1184267005919 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 1184267005920 muropeptide transporter; Validated; Region: ampG; cl17669 1184267005921 muropeptide transporter; Validated; Region: ampG; cl17669 1184267005922 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 1184267005923 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 1184267005924 binding surface 1184267005925 TPR motif; other site 1184267005926 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 1184267005927 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 1184267005928 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1184267005929 catalytic residue [active] 1184267005930 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 1184267005931 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1184267005932 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 1184267005933 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1184267005934 Amidase; Region: Amidase; cl11426 1184267005935 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 1184267005936 active site 1184267005937 Zn binding site [ion binding]; other site 1184267005938 voltage-dependent potassium channel beta subunit, animal; Region: Kv_beta; TIGR01293 1184267005939 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 1184267005940 active site 1184267005941 catalytic tetrad [active] 1184267005942 flagellin; Provisional; Region: PRK12802 1184267005943 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1184267005944 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1184267005945 flagellin; Provisional; Region: PRK12802 1184267005946 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1184267005947 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1184267005948 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 1184267005949 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1184267005950 Zn2+ binding site [ion binding]; other site 1184267005951 Mg2+ binding site [ion binding]; other site 1184267005952 Domain of unknown function (DUF4097); Region: DUF4097; pfam13349 1184267005953 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 1184267005954 Predicted membrane protein [Function unknown]; Region: COG4709 1184267005955 Predicted transcriptional regulators [Transcription]; Region: COG1695 1184267005956 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 1184267005957 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1184267005958 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1184267005959 Prominin; Region: Prominin; pfam05478 1184267005960 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 1184267005961 CheD chemotactic sensory transduction; Region: CheD; cl00810 1184267005962 putative acyltransferase; Provisional; Region: PRK05790 1184267005963 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 1184267005964 dimer interface [polypeptide binding]; other site 1184267005965 active site 1184267005966 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1184267005967 Peptidase family M23; Region: Peptidase_M23; pfam01551 1184267005968 Protein phosphatase 2C; Region: PP2C; pfam00481 1184267005969 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 1184267005970 active site 1184267005971 TonB C terminal; Region: TonB_2; pfam13103 1184267005972 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 1184267005973 TPP-binding site [chemical binding]; other site 1184267005974 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 1184267005975 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1184267005976 Eukaryotic protein of unknown function (DUF829); Region: DUF829; pfam05705 1184267005977 short chain dehydrogenase; Provisional; Region: PRK06914 1184267005978 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 1184267005979 NADP binding site [chemical binding]; other site 1184267005980 active site 1184267005981 steroid binding site; other site 1184267005982 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 1184267005983 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 1184267005984 phosphoglycolate phosphatase; Provisional; Region: PRK13222 1184267005985 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 1184267005986 motif II; other site 1184267005987 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 1184267005988 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1184267005989 Walker A/P-loop; other site 1184267005990 ATP binding site [chemical binding]; other site 1184267005991 Q-loop/lid; other site 1184267005992 ABC transporter signature motif; other site 1184267005993 Walker B; other site 1184267005994 D-loop; other site 1184267005995 H-loop/switch region; other site 1184267005996 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 1184267005997 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 1184267005998 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1184267005999 Walker A/P-loop; other site 1184267006000 ATP binding site [chemical binding]; other site 1184267006001 Q-loop/lid; other site 1184267006002 ABC transporter signature motif; other site 1184267006003 Walker B; other site 1184267006004 D-loop; other site 1184267006005 H-loop/switch region; other site 1184267006006 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 1184267006007 PilZ domain; Region: PilZ; pfam07238 1184267006008 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267006009 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267006010 active site 1184267006011 phosphorylation site [posttranslational modification] 1184267006012 intermolecular recognition site; other site 1184267006013 dimerization interface [polypeptide binding]; other site 1184267006014 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1184267006015 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1184267006016 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1184267006017 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1184267006018 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 1184267006019 catalytic loop [active] 1184267006020 iron binding site [ion binding]; other site 1184267006021 Putative methyltransferase; Region: Methyltransf_4; cl17290 1184267006022 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267006023 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267006024 active site 1184267006025 phosphorylation site [posttranslational modification] 1184267006026 intermolecular recognition site; other site 1184267006027 dimerization interface [polypeptide binding]; other site 1184267006028 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 1184267006029 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1184267006030 metal binding site [ion binding]; metal-binding site 1184267006031 active site 1184267006032 I-site; other site 1184267006033 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1184267006034 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1184267006035 HIGH motif; other site 1184267006036 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1184267006037 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1184267006038 active site 1184267006039 KMSKS motif; other site 1184267006040 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1184267006041 tRNA binding surface [nucleotide binding]; other site 1184267006042 arginine decarboxylase; Provisional; Region: PRK05354 1184267006043 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 1184267006044 dimer interface [polypeptide binding]; other site 1184267006045 active site 1184267006046 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1184267006047 catalytic residues [active] 1184267006048 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 1184267006049 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 1184267006050 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 1184267006051 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 1184267006052 dimer interface [polypeptide binding]; other site 1184267006053 conserved gate region; other site 1184267006054 putative PBP binding loops; other site 1184267006055 ABC-ATPase subunit interface; other site 1184267006056 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 1184267006057 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 1184267006058 dimer interface [polypeptide binding]; other site 1184267006059 conserved gate region; other site 1184267006060 putative PBP binding loops; other site 1184267006061 ABC-ATPase subunit interface; other site 1184267006062 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1184267006063 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 1184267006064 agmatinase; Region: agmatinase; TIGR01230 1184267006065 Agmatinase and related proteins; Region: Agmatinase-like_2; cd11593 1184267006066 putative active site [active] 1184267006067 Mn binding site [ion binding]; other site 1184267006068 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 1184267006069 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1184267006070 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1184267006071 Bacterial transcriptional repressor; Region: TetR; pfam13972 1184267006072 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1184267006073 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267006074 putative catalytic site [active] 1184267006075 putative metal binding site [ion binding]; other site 1184267006076 putative phosphate binding site [ion binding]; other site 1184267006077 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 1184267006078 C-terminal peptidase (prc); Region: prc; TIGR00225 1184267006079 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 1184267006080 protein binding site [polypeptide binding]; other site 1184267006081 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1184267006082 Catalytic dyad [active] 1184267006083 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1184267006084 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 1184267006085 NAD(P) binding site [chemical binding]; other site 1184267006086 active site 1184267006087 phenylalanine 4-monooxygenase; Provisional; Region: PRK14056 1184267006088 Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan...; Region: arom_aa_hydroxylase; cd00361 1184267006089 cofactor binding site; other site 1184267006090 metal binding site [ion binding]; metal-binding site 1184267006091 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1184267006092 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1184267006093 Haemagglutinin; Region: Hemagglutinin; pfam00509 1184267006094 homogentisate 1,2-dioxygenase; Region: HgmA; cl17306 1184267006095 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 1184267006096 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 1184267006097 dimer interface [polypeptide binding]; other site 1184267006098 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 1184267006099 active site 1184267006100 Fe binding site [ion binding]; other site 1184267006101 Double zinc ribbon; Region: DZR; pfam12773 1184267006102 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 1184267006103 putative DNA binding site [nucleotide binding]; other site 1184267006104 putative Zn2+ binding site [ion binding]; other site 1184267006105 PIF1-like helicase; Region: PIF1; pfam05970 1184267006106 AAA domain; Region: AAA_30; pfam13604 1184267006107 Helicase; Region: Herpes_Helicase; pfam02689 1184267006108 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 1184267006109 active site residue [active] 1184267006110 5' nucleotidase family; Region: 5_nucleotid; cl17687 1184267006111 Uncharacterized conserved protein [Function unknown]; Region: COG5495 1184267006112 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 1184267006113 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 1184267006114 oligomerization interface [polypeptide binding]; other site 1184267006115 active site 1184267006116 metal binding site [ion binding]; metal-binding site 1184267006117 pantoate--beta-alanine ligase; Region: panC; TIGR00018 1184267006118 pantoate--beta-alanine ligase; Reviewed; Region: panC; PRK00380 1184267006119 active site 1184267006120 nucleotide binding site [chemical binding]; other site 1184267006121 HIGH motif; other site 1184267006122 KMSKS motif; other site 1184267006123 phosphopantothenoylcysteine decarboxylase; Validated; Region: PRK07313 1184267006124 Flavoprotein; Region: Flavoprotein; pfam02441 1184267006125 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 1184267006126 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1184267006127 nucleotide binding site [chemical binding]; other site 1184267006128 Type III pantothenate kinase; Region: Pan_kinase; cl17198 1184267006129 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 1184267006130 tetramerization interface [polypeptide binding]; other site 1184267006131 active site 1184267006132 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1184267006133 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 1184267006134 Di-iron ligands [ion binding]; other site 1184267006135 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 1184267006136 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 1184267006137 active site 1184267006138 catalytic residues [active] 1184267006139 metal binding site [ion binding]; metal-binding site 1184267006140 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 1184267006141 carboxyltransferase (CT) interaction site; other site 1184267006142 biotinylation site [posttranslational modification]; other site 1184267006143 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 1184267006144 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1184267006145 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1184267006146 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 1184267006147 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 1184267006148 enoyl-CoA hydratase; Provisional; Region: PRK05995 1184267006149 substrate binding site [chemical binding]; other site 1184267006150 oxyanion hole (OAH) forming residues; other site 1184267006151 trimer interface [polypeptide binding]; other site 1184267006152 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 1184267006153 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1184267006154 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 1184267006155 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 1184267006156 S-adenosylmethionine binding site [chemical binding]; other site 1184267006157 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 1184267006158 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 1184267006159 non-specific DNA binding site [nucleotide binding]; other site 1184267006160 salt bridge; other site 1184267006161 sequence-specific DNA binding site [nucleotide binding]; other site 1184267006162 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 1184267006163 Interdomain contacts; other site 1184267006164 Cytokine receptor motif; other site 1184267006165 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 1184267006166 FMN binding site [chemical binding]; other site 1184267006167 dimer interface [polypeptide binding]; other site 1184267006168 Protein of unknown function (DUF3015); Region: DUF3015; pfam11220 1184267006169 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 1184267006170 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 1184267006171 cleavage site 1184267006172 active site 1184267006173 substrate binding sites [chemical binding]; other site 1184267006174 Transcriptional regulator [Transcription]; Region: LysR; COG0583 1184267006175 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 1184267006176 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 1184267006177 dimerization interface [polypeptide binding]; other site 1184267006178 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 1184267006179 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 1184267006180 spermidine synthase; Provisional; Region: PRK00811 1184267006181 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 1184267006182 S-adenosylmethionine binding site [chemical binding]; other site 1184267006183 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1184267006184 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1184267006185 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1184267006186 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1184267006187 Active site serine [active] 1184267006188 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 1184267006189 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 1184267006190 proline aminopeptidase P II; Provisional; Region: PRK10879 1184267006191 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 1184267006192 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 1184267006193 active site 1184267006194 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1184267006195 active site 1184267006196 nucleophile elbow; other site 1184267006197 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1184267006198 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 1184267006199 S-adenosylmethionine binding site [chemical binding]; other site 1184267006200 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1184267006201 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1184267006202 substrate binding pocket [chemical binding]; other site 1184267006203 chain length determination region; other site 1184267006204 substrate-Mg2+ binding site; other site 1184267006205 catalytic residues [active] 1184267006206 aspartate-rich region 1; other site 1184267006207 active site lid residues [active] 1184267006208 aspartate-rich region 2; other site 1184267006209 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1184267006210 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 1184267006211 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 1184267006212 generic binding surface II; other site 1184267006213 generic binding surface I; other site 1184267006214 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 1184267006215 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1184267006216 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1184267006217 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 1184267006218 NifU-like domain; Region: NifU; pfam01106 1184267006219 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1184267006220 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 1184267006221 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1184267006222 catalytic residue [active] 1184267006223 FeS assembly protein SufD; Region: sufD; TIGR01981 1184267006224 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 1184267006225 FeS assembly ATPase SufC; Region: sufC; TIGR01978 1184267006226 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 1184267006227 Walker A/P-loop; other site 1184267006228 ATP binding site [chemical binding]; other site 1184267006229 Q-loop/lid; other site 1184267006230 ABC transporter signature motif; other site 1184267006231 Walker B; other site 1184267006232 D-loop; other site 1184267006233 H-loop/switch region; other site 1184267006234 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 1184267006235 putative ABC transporter; Region: ycf24; CHL00085 1184267006236 Rrf2 family protein; Region: rrf2_super; TIGR00738 1184267006237 Transcriptional regulator; Region: Rrf2; pfam02082 1184267006238 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 1184267006239 active site 1184267006240 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 1184267006241 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 1184267006242 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1184267006243 TolR protein; Region: tolR; TIGR02801 1184267006244 TonB C terminal; Region: TonB_2; pfam13103 1184267006245 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 1184267006246 TolB amino-terminal domain; Region: TolB_N; pfam04052 1184267006247 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1184267006248 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1184267006249 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1184267006250 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1184267006251 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 1184267006252 substrate binding site [chemical binding]; other site 1184267006253 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 1184267006254 active site 1184267006255 acetyl-CoA acetyltransferase; Provisional; Region: PRK09268 1184267006256 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 1184267006257 dimer interface [polypeptide binding]; other site 1184267006258 active site 1184267006259 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 1184267006260 active site 1184267006261 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1184267006262 hopanoid-associated sugar epimerase; Region: HpnA; TIGR03466 1184267006263 uncharacterized subgroup of aldehyde reductase and flavonoid reductase related proteins, extended (e) SDRs; Region: AR_FR_like_1_SDR_e; cd05228 1184267006264 putative NADP binding site [chemical binding]; other site 1184267006265 putative substrate binding site [chemical binding]; other site 1184267006266 active site 1184267006267 Transglycosylase; Region: Transgly; pfam00912 1184267006268 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1184267006269 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1184267006270 G1 box; other site 1184267006271 putative GEF interaction site [polypeptide binding]; other site 1184267006272 GTP/Mg2+ binding site [chemical binding]; other site 1184267006273 Switch I region; other site 1184267006274 G2 box; other site 1184267006275 G3 box; other site 1184267006276 Switch II region; other site 1184267006277 G4 box; other site 1184267006278 G5 box; other site 1184267006279 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 1184267006280 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 1184267006281 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1184267006282 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 1184267006283 FMN binding site [chemical binding]; other site 1184267006284 active site 1184267006285 catalytic residues [active] 1184267006286 substrate binding site [chemical binding]; other site 1184267006287 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 1184267006288 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006289 FeS/SAM binding site; other site 1184267006290 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 1184267006291 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006292 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 1184267006293 FeS/SAM binding site; other site 1184267006294 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006295 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 1184267006296 FeS/SAM binding site; other site 1184267006297 Phosphotransferase enzyme family; Region: APH; pfam01636 1184267006298 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 1184267006299 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cd00229 1184267006300 oxyanion hole [active] 1184267006301 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 1184267006302 active site 1184267006303 oxyanion hole [active] 1184267006304 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1184267006305 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 1184267006306 binding surface 1184267006307 TPR motif; other site 1184267006308 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 1184267006309 binding surface 1184267006310 TPR motif; other site 1184267006311 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 1184267006312 active site 1184267006313 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cd00229 1184267006314 active site 1184267006315 oxyanion hole [active] 1184267006316 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 1184267006317 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 1184267006318 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006319 FeS/SAM binding site; other site 1184267006320 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 1184267006321 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006322 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 1184267006323 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006324 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006325 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 1184267006326 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006327 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 1184267006328 FeS/SAM binding site; other site 1184267006329 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 1184267006330 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1184267006331 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 1184267006332 Ligand binding site; other site 1184267006333 Putative Catalytic site; other site 1184267006334 DXD motif; other site 1184267006335 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cd02062 1184267006336 FMN binding site [chemical binding]; other site 1184267006337 dimer interface [polypeptide binding]; other site 1184267006338 YceG-like family; Region: YceG; pfam02618 1184267006339 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1184267006340 dimerization interface [polypeptide binding]; other site 1184267006341 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 1184267006342 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 1184267006343 NAD(P) binding site [chemical binding]; other site 1184267006344 catalytic residues [active] 1184267006345 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 1184267006346 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 1184267006347 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 1184267006348 Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE)-like; Region: M20_ArgE_DapE_like; cd08659 1184267006349 metal binding site [ion binding]; metal-binding site 1184267006350 dimer interface [polypeptide binding]; other site 1184267006351 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 1184267006352 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 1184267006353 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1184267006354 catalytic residue [active] 1184267006355 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 1184267006356 binding surface 1184267006357 TPR motif; other site 1184267006358 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 1184267006359 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 1184267006360 binding surface 1184267006361 TPR motif; other site 1184267006362 TPR repeat; Region: TPR_11; pfam13414 1184267006363 TPR repeat; Region: TPR_11; pfam13414 1184267006364 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 1184267006365 binding surface 1184267006366 TPR motif; other site 1184267006367 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1184267006368 active site 1184267006369 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 1184267006370 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 1184267006371 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 1184267006372 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 1184267006373 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 1184267006374 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 1184267006375 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 1184267006376 ATP binding site [chemical binding]; other site 1184267006377 Walker A motif; other site 1184267006378 hexamer interface [polypeptide binding]; other site 1184267006379 Walker B motif; other site 1184267006380 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 1184267006381 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1184267006382 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267006383 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267006384 active site 1184267006385 phosphorylation site [posttranslational modification] 1184267006386 intermolecular recognition site; other site 1184267006387 dimerization interface [polypeptide binding]; other site 1184267006388 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1184267006389 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 1184267006390 ring oligomerisation interface [polypeptide binding]; other site 1184267006391 ATP/Mg binding site [chemical binding]; other site 1184267006392 stacking interactions; other site 1184267006393 hinge regions; other site 1184267006394 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 1184267006395 oligomerisation interface [polypeptide binding]; other site 1184267006396 mobile loop; other site 1184267006397 roof hairpin; other site 1184267006398 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 1184267006399 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 1184267006400 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cd00190 1184267006401 cleavage site 1184267006402 active site 1184267006403 substrate binding sites [chemical binding]; other site 1184267006404 Pirin-related protein [General function prediction only]; Region: COG1741 1184267006405 Pirin; Region: Pirin; pfam02678 1184267006406 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1184267006407 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1184267006408 dimerization interface [polypeptide binding]; other site 1184267006409 DPS ferroxidase diiron center [ion binding]; other site 1184267006410 ion pore; other site 1184267006411 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1184267006412 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 1184267006413 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 1184267006414 CoenzymeA binding site [chemical binding]; other site 1184267006415 subunit interaction site [polypeptide binding]; other site 1184267006416 PHB binding site; other site 1184267006417 DNA N-6-adenine-methyltransferase (Dam); Region: Dam; cl05442 1184267006418 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1184267006419 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 1184267006420 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 1184267006421 active site 1184267006422 FMN binding site [chemical binding]; other site 1184267006423 substrate binding site [chemical binding]; other site 1184267006424 3Fe-4S cluster binding site [ion binding]; other site 1184267006425 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 1184267006426 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1184267006427 putative substrate translocation pore; other site 1184267006428 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 1184267006429 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 1184267006430 active site 1184267006431 catalytic residues [active] 1184267006432 DNA binding site [nucleotide binding] 1184267006433 Int/Topo IB signature motif; other site 1184267006434 Helix-turn-helix domain; Region: HTH_36; pfam13730 1184267006435 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1184267006436 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 1184267006437 non-specific DNA binding site [nucleotide binding]; other site 1184267006438 salt bridge; other site 1184267006439 sequence-specific DNA binding site [nucleotide binding]; other site 1184267006440 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1184267006441 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 1184267006442 non-specific DNA binding site [nucleotide binding]; other site 1184267006443 salt bridge; other site 1184267006444 sequence-specific DNA binding site [nucleotide binding]; other site 1184267006445 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 1184267006446 D5 N terminal like; Region: D5_N; smart00885 1184267006447 phage/plasmid primase, P4 family, C-terminal domain; Region: primase_Cterm; TIGR01613 1184267006448 Helix-turn-helix domain; Region: HTH_17; pfam12728 1184267006449 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 1184267006450 active site 1184267006451 catalytic residues [active] 1184267006452 DNA binding site [nucleotide binding] 1184267006453 Int/Topo IB signature motif; other site 1184267006454 HNH endonuclease; Region: HNH; pfam01844 1184267006455 active site 1184267006456 AAA domain; Region: AAA_21; pfam13304 1184267006457 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1184267006458 ABC transporter signature motif; other site 1184267006459 Walker B; other site 1184267006460 D-loop; other site 1184267006461 H-loop/switch region; other site 1184267006462 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 1184267006463 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 1184267006464 putative NAD(P) binding site [chemical binding]; other site 1184267006465 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 1184267006466 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 1184267006467 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 1184267006468 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 1184267006469 active site 1184267006470 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 1184267006471 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 1184267006472 cleavage site 1184267006473 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 1184267006474 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 1184267006475 HflX GTPase family; Region: HflX; cd01878 1184267006476 G1 box; other site 1184267006477 GTP/Mg2+ binding site [chemical binding]; other site 1184267006478 Switch I region; other site 1184267006479 G2 box; other site 1184267006480 G3 box; other site 1184267006481 Switch II region; other site 1184267006482 G4 box; other site 1184267006483 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 1184267006484 putative catalytic site [active] 1184267006485 putative metal binding site [ion binding]; other site 1184267006486 putative phosphate binding site [ion binding]; other site 1184267006487 HipA N-terminal domain; Region: Couple_hipA; pfam13657 1184267006488 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 1184267006489 HipA-like N-terminal domain; Region: HipA_N; pfam07805 1184267006490 HipA-like C-terminal domain; Region: HipA_C; pfam07804 1184267006491 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 1184267006492 non-specific DNA binding site [nucleotide binding]; other site 1184267006493 salt bridge; other site 1184267006494 sequence-specific DNA binding site [nucleotide binding]; other site 1184267006495 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 1184267006496 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 1184267006497 ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]; Region: AbcD; COG2011 1184267006498 dimer interface [polypeptide binding]; other site 1184267006499 conserved gate region; other site 1184267006500 ABC-ATPase subunit interface; other site 1184267006501 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1184267006502 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 1184267006503 Walker A/P-loop; other site 1184267006504 ATP binding site [chemical binding]; other site 1184267006505 Q-loop/lid; other site 1184267006506 ABC transporter signature motif; other site 1184267006507 Walker B; other site 1184267006508 D-loop; other site 1184267006509 H-loop/switch region; other site 1184267006510 Protein of unknown function (DUF3750); Region: DUF3750; pfam12570 1184267006511 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 1184267006512 active site 1184267006513 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 1184267006514 putative binding surface; other site 1184267006515 active site 1184267006516 CHASE3 domain; Region: CHASE3; pfam05227 1184267006517 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267006518 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 1184267006519 dimer interface [polypeptide binding]; other site 1184267006520 phosphorylation site [posttranslational modification] 1184267006521 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 1184267006522 ATP binding site [chemical binding]; other site 1184267006523 Mg2+ binding site [ion binding]; other site 1184267006524 G-X-G motif; other site 1184267006525 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267006526 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267006527 active site 1184267006528 phosphorylation site [posttranslational modification] 1184267006529 intermolecular recognition site; other site 1184267006530 dimerization interface [polypeptide binding]; other site 1184267006531 Protein of unknown function (DUF3187); Region: DUF3187; pfam11383 1184267006532 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1184267006533 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 1184267006534 non-specific DNA binding site [nucleotide binding]; other site 1184267006535 salt bridge; other site 1184267006536 sequence-specific DNA binding site [nucleotide binding]; other site 1184267006537 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in 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 1184267006538 PAS domain; Region: PAS_9; pfam13426 1184267006539 putative active site [active] 1184267006540 heme pocket [chemical binding]; other site 1184267006541 delta-60 repeat domain; Region: delta_60_rpt; TIGR02608 1184267006542 delta-60 repeat domain; Region: delta_60_rpt; TIGR02608 1184267006543 delta-60 repeat domain; Region: delta_60_rpt; TIGR02608 1184267006544 Response regulator receiver domain; Region: Response_reg; pfam00072 1184267006545 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 1184267006546 active site 1184267006547 phosphorylation site [posttranslational modification] 1184267006548 intermolecular recognition site; other site 1184267006549 dimerization interface [polypeptide binding]; other site 1184267006550 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 1184267006551 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 1184267006552 putative active site [active] 1184267006553 catalytic site [active] 1184267006554 putative metal binding site [ion binding]; other site 1184267006555 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 1184267006556 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 1184267006557 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 1184267006558 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 1184267006559 dimer interface [polypeptide binding]; other site 1184267006560 conserved gate region; other site 1184267006561 putative PBP binding loops; other site 1184267006562 ABC-ATPase subunit interface; other site 1184267006563 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 1184267006564 dimer interface [polypeptide binding]; other site 1184267006565 conserved gate region; other site 1184267006566 putative PBP binding loops; other site 1184267006567 ABC-ATPase subunit interface; other site 1184267006568 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 1184267006569 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 1184267006570 Walker A/P-loop; other site 1184267006571 ATP binding site [chemical binding]; other site 1184267006572 Q-loop/lid; other site 1184267006573 ABC transporter signature motif; other site 1184267006574 Walker B; other site 1184267006575 D-loop; other site 1184267006576 H-loop/switch region; other site 1184267006577 Rhomboid family; Region: Rhomboid; cl11446 1184267006578 Plant protein of unknown function (DUF946); Region: DUF946; pfam06101 1184267006579 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1184267006580 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 1184267006581 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1184267006582 catalytic residue [active] 1184267006583 Putative 2OG-Fe(II) oxygenase; Region: 2OG-FeII_Oxy_5; cl17879 1184267006584 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 1184267006585 catalytic residues [active] 1184267006586 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 1184267006587 active site 1184267006588 Zn binding site [ion binding]; other site 1184267006589 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 1184267006590 active site 1184267006591 catalytic residues [active] 1184267006592 DNA binding site [nucleotide binding] 1184267006593 Int/Topo IB signature motif; other site 1184267006594 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 1184267006595 salt bridge; other site 1184267006596 non-specific DNA binding site [nucleotide binding]; other site 1184267006597 sequence-specific DNA binding site [nucleotide binding]; other site 1184267006598 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1184267006599 Peptidase family M23; Region: Peptidase_M23; pfam01551 1184267006600 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 1184267006601 Mg2+ binding site [ion binding]; other site 1184267006602 G-X-G motif; other site 1184267006603 Domain of unknown function (DUF4325); Region: DUF4325; pfam14213 1184267006604 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1184267006605 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 1184267006606 ATP binding site [chemical binding]; other site 1184267006607 G-X-G motif; other site 1184267006608 N-acetyltransferase; Region: Acetyltransf_2; cl00949 1184267006609 EamA-like transporter family; Region: EamA; pfam00892 1184267006610 EamA-like transporter family; Region: EamA; pfam00892 1184267006611 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 1184267006612 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 1184267006613 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 1184267006614 intracellular protease, PfpI family; Region: PfpI; TIGR01382 1184267006615 proposed catalytic triad [active] 1184267006616 conserved cys residue [active] 1184267006617 Transposase IS200 like; Region: Y1_Tnp; cl00848 1184267006618 acyl-coenzyme A oxidase; Region: PLN02526 1184267006619 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 1184267006620 active site 1184267006621 Predicted membrane protein (DUF2177); Region: DUF2177; pfam09945 1184267006622 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 1184267006623 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1184267006624 NAD(P) binding site [chemical binding]; other site 1184267006625 active site 1184267006626 Protein of unknown function, DUF486; Region: DUF486; cl01236 1184267006627 Asparagine synthase; Region: Asn_synthase; pfam00733 1184267006628 OsmC-like protein; Region: OsmC; cl00767 1184267006629 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1184267006630 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 1184267006631 active site 1184267006632 metal binding site [ion binding]; metal-binding site 1184267006633 Protein of unknown function (DUF962); Region: DUF962; cl01879 1184267006634 EamA-like transporter family; Region: EamA; pfam00892 1184267006635 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1184267006636 EamA-like transporter family; Region: EamA; pfam00892 1184267006637 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 1184267006638 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 1184267006639 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 1184267006640 putative DNA binding site [nucleotide binding]; other site 1184267006641 putative Zn2+ binding site [ion binding]; other site 1184267006642 AsnC family; Region: AsnC_trans_reg; pfam01037 1184267006643 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 1184267006644 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 1184267006645 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 1184267006646 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 1184267006647 homodimer interface [polypeptide binding]; other site 1184267006648 substrate-cofactor binding pocket; other site 1184267006649 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267006650 catalytic residue [active] 1184267006651 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1184267006652 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 1184267006653 dimer interface [polypeptide binding]; other site 1184267006654 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1184267006655 catalytic residue [active] 1184267006656 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 1184267006657 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1184267006658 putative active site [active] 1184267006659 catalytic triad [active] 1184267006660 putative dimer interface [polypeptide binding]; other site 1184267006661 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 1184267006662 malate dehydrogenase; Reviewed; Region: PRK06223 1184267006663 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1184267006664 NAD(P) binding site [chemical binding]; other site 1184267006665 dimer interface [polypeptide binding]; other site 1184267006666 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1184267006667 substrate binding site [chemical binding]; other site 1184267006668 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1184267006669 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1184267006670 CoA-ligase; Region: Ligase_CoA; pfam00549 1184267006671 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1184267006672 CoA binding domain; Region: CoA_binding; smart00881 1184267006673 CoA-ligase; Region: Ligase_CoA; pfam00549 1184267006674 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 1184267006675 active site 1184267006676 multimer interface [polypeptide binding]; other site 1184267006677 TRAM domain; Region: TRAM; cl01282 1184267006678 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 1184267006679 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1184267006680 TPR repeat; Region: TPR_11; pfam13414 1184267006681 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 1184267006682 binding surface 1184267006683 TPR motif; other site 1184267006684 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1184267006685 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 1184267006686 binding surface 1184267006687 TPR motif; other site 1184267006688 Helix-turn-helix domain; Region: HTH_25; pfam13413 1184267006689 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 1184267006690 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1184267006691 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 1184267006692 catalytic loop [active] 1184267006693 iron binding site [ion binding]; other site 1184267006694 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 1184267006695 active site 1184267006696 catalytic site [active] 1184267006697 substrate binding site [chemical binding]; other site 1184267006698 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 1184267006699 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1184267006700 NAD synthetase; Provisional; Region: PRK13981 1184267006701 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 1184267006702 multimer interface [polypeptide binding]; other site 1184267006703 active site 1184267006704 catalytic triad [active] 1184267006705 protein interface 1 [polypeptide binding]; other site 1184267006706 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 1184267006707 homodimer interface [polypeptide binding]; other site 1184267006708 NAD binding pocket [chemical binding]; other site 1184267006709 ATP binding pocket [chemical binding]; other site 1184267006710 Mg binding site [ion binding]; other site 1184267006711 active-site loop [active] 1184267006712 Uncharacterized conserved protein (DUF2203); Region: DUF2203; pfam09969 1184267006713 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 1184267006714 TPR motif; other site 1184267006715 binding surface 1184267006716 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 1184267006717 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1184267006718 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 1184267006719 FeS/SAM binding site; other site 1184267006720 TRAM domain; Region: TRAM; pfam01938 1184267006721 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 1184267006722 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 1184267006723 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1184267006724 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 1184267006725 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 1184267006726 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 1184267006727 active site 1184267006728 (T/H)XGH motif; other site 1184267006729 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 1184267006730 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1184267006731 GTP1/OBG; Region: GTP1_OBG; pfam01018 1184267006732 Obg GTPase; Region: Obg; cd01898 1184267006733 G1 box; other site 1184267006734 GTP/Mg2+ binding site [chemical binding]; other site 1184267006735 Switch I region; other site 1184267006736 G2 box; other site 1184267006737 G3 box; other site 1184267006738 Switch II region; other site 1184267006739 G4 box; other site 1184267006740 G5 box; other site 1184267006741 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1184267006742 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1184267006743 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 1184267006744 Fic family protein [Function unknown]; Region: COG3177 1184267006745 Predicted transcriptional regulator [Transcription]; Region: COG3355 1184267006746 choice-of-anchor A domain; Region: choice_anch_A; TIGR04215 1184267006747 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 1184267006748 Ligand Binding Site [chemical binding]; other site 1184267006749 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 1184267006750 S-adenosylmethionine binding site [chemical binding]; other site 1184267006751 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 1184267006752 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1184267006753 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 1184267006754 Di-iron ligands [ion binding]; other site 1184267006755 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 1184267006756 ribonuclease G; Provisional; Region: PRK11712 1184267006757 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 1184267006758 homodimer interface [polypeptide binding]; other site 1184267006759 oligonucleotide binding site [chemical binding]; other site 1184267006760 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 1184267006761 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 1184267006762 Walker A motif; other site 1184267006763 ATP binding site [chemical binding]; other site 1184267006764 Walker B motif; other site 1184267006765 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 1184267006766 intersubunit interface [polypeptide binding]; other site 1184267006767 active site 1184267006768 catalytic residue [active] 1184267006769 pyrimidine-nucleoside phosphorylase; Region: Y_phosphoryl; TIGR02644 1184267006770 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 1184267006771 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 1184267006772 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 1184267006773 purine nucleoside phosphorylase; Provisional; Region: PRK08202 1184267006774 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 1184267006775 catalytic triad [active] 1184267006776 putative active site [active] 1184267006777 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 1184267006778 AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a...; Region: AsnRS_cyto_like_N; cd04323 1184267006779 putative dimer interface [polypeptide binding]; other site 1184267006780 putative anticodon binding site; other site 1184267006781 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 1184267006782 homodimer interface [polypeptide binding]; other site 1184267006783 motif 1; other site 1184267006784 motif 2; other site 1184267006785 active site 1184267006786 motif 3; other site 1184267006787 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 1184267006788 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1184267006789 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1184267006790 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 1184267006791 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1184267006792 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1184267006793 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1184267006794 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 1184267006795 carboxyltransferase (CT) interaction site; other site 1184267006796 biotinylation site [posttranslational modification]; other site 1184267006797 Predicted membrane protein [Function unknown]; Region: COG2259 1184267006798 Sec-independent protein translocase protein (TatC); Region: TatC; pfam00902 1184267006799 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]; Region: VirB11; COG0630 1184267006800 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 1184267006801 ATP binding site [chemical binding]; other site 1184267006802 Walker A motif; other site 1184267006803 hexamer interface [polypeptide binding]; other site 1184267006804 Walker B motif; other site 1184267006805 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1184267006806 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1184267006807 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1184267006808 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1184267006809 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1184267006810 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1184267006811 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 1184267006812 Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate...; Region: PRTase_typeII; cl17275 1184267006813 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 1184267006814 HemN C-terminal domain; Region: HemN_C; pfam06969 1184267006815 GrpE; Region: GrpE; pfam01025 1184267006816 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 1184267006817 dimer interface [polypeptide binding]; other site 1184267006818 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1184267006819 chaperone protein DnaJ; Provisional; Region: PRK14283 1184267006820 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 1184267006821 HSP70 interaction site [polypeptide binding]; other site 1184267006822 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1184267006823 substrate binding site [polypeptide binding]; other site 1184267006824 dimer interface [polypeptide binding]; other site 1184267006825 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1184267006826 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 1184267006827 putative ligand binding site [chemical binding]; other site 1184267006828 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 1184267006829 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 1184267006830 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1184267006831 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1184267006832 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 1184267006833 Walker A motif; other site 1184267006834 ATP binding site [chemical binding]; other site 1184267006835 Walker B motif; other site 1184267006836 arginine finger; other site 1184267006837 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1184267006838 Protein of unknown function (DUF972); Region: DUF972; pfam06156 1184267006839 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1184267006840 active site 1184267006841 nucleophile elbow; other site 1184267006842 putative acetyltransferase; Provisional; Region: PRK03624 1184267006843 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1184267006844 Coenzyme A binding pocket [chemical binding]; other site 1184267006845 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 1184267006846 oxyanion hole [active] 1184267006847 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 1184267006848 catalytic triad [active] 1184267006849 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 1184267006850 active site 1184267006851 catalytic residues [active] 1184267006852 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 1184267006853 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 1184267006854 Ligand Binding Site [chemical binding]; other site 1184267006855 Vitamin K-dependent gamma-carboxylase; Region: VKG_Carbox; cl02773 1184267006856 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1184267006857 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1184267006858 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 1184267006859 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1184267006860 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1184267006861 NADH-ubiquinone oxidoreductase chain 4, amino terminus; Region: Oxidored_q5_N; pfam01059 1184267006862 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1184267006863 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1184267006864 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1184267006865 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1184267006866 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1184267006867 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1184267006868 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 1184267006869 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1184267006870 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1184267006871 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 1184267006872 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1184267006873 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 1184267006874 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 1184267006875 ATP binding site [chemical binding]; other site 1184267006876 putative Mg++ binding site [ion binding]; other site 1184267006877 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 1184267006878 nucleotide binding region [chemical binding]; other site 1184267006879 ATP-binding site [chemical binding]; other site 1184267006880 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1184267006881 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 1184267006882 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 1184267006883 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1184267006884 gamma subunit interface [polypeptide binding]; other site 1184267006885 epsilon subunit interface [polypeptide binding]; other site 1184267006886 LBP interface [polypeptide binding]; other site 1184267006887 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1184267006888 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1184267006889 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 1184267006890 alpha subunit interaction interface [polypeptide binding]; other site 1184267006891 Walker A motif; other site 1184267006892 ATP binding site [chemical binding]; other site 1184267006893 Walker B motif; other site 1184267006894 inhibitor binding site; inhibition site 1184267006895 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1184267006896 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1184267006897 core domain interface [polypeptide binding]; other site 1184267006898 delta subunit interface [polypeptide binding]; other site 1184267006899 epsilon subunit interface [polypeptide binding]; other site 1184267006900 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1184267006901 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1184267006902 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 1184267006903 beta subunit interaction interface [polypeptide binding]; other site 1184267006904 Walker A motif; other site 1184267006905 ATP binding site [chemical binding]; other site 1184267006906 Walker B motif; other site 1184267006907 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1184267006908 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 1184267006909 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1184267006910 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1184267006911 ATP synthase B/B' CF(0); Region: ATP-synt_B; pfam00430 1184267006912 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 1184267006913 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1184267006914 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 1184267006915 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1184267006916 ParB-like nuclease domain; Region: ParBc; pfam02195 1184267006917 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1184267006918 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 1184267006919 P-loop; other site 1184267006920 Magnesium ion binding site [ion binding]; other site 1184267006921 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 1184267006922 Magnesium ion binding site [ion binding]; other site 1184267006923 hypothetical protein; Provisional; Region: PRK11281 1184267006924 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; cl17726 1184267006925 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1184267006926 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1184267006927 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 1184267006928 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1184267006929 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 1184267006930 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1184267006931 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1184267006932 G1 box; other site 1184267006933 GTP/Mg2+ binding site [chemical binding]; other site 1184267006934 Switch I region; other site 1184267006935 G2 box; other site 1184267006936 Switch II region; other site 1184267006937 G3 box; other site 1184267006938 G4 box; other site 1184267006939 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1184267006940 jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta...; Region: jag_KH; cd02414 1184267006941 G-X-X-G motif; other site 1184267006942 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 1184267006943 RxxxH motif; other site 1184267006944 membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Region: yidC_nterm; TIGR03593 1184267006945 Preprotein translocase subunit YidC [Intracellular trafficking and secretion]; Region: YidC; COG0706 1184267006946 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1184267006947 Ribonuclease P; Region: Ribonuclease_P; cl00457 1184267006948 Ribonuclease P; Region: Ribonuclease_P; cl00457 1184267006949 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399