-- dump date 20140619_164051 -- class Genbank::misc_feature -- table misc_feature_note -- id note 387092000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 387092000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 387092000003 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 387092000004 Walker A motif; other site 387092000005 ATP binding site [chemical binding]; other site 387092000006 Walker B motif; other site 387092000007 arginine finger; other site 387092000008 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 387092000009 DnaA box-binding interface [nucleotide binding]; other site 387092000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 387092000011 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 387092000012 putative DNA binding surface [nucleotide binding]; other site 387092000013 dimer interface [polypeptide binding]; other site 387092000014 beta-clamp/clamp loader binding surface; other site 387092000015 beta-clamp/translesion DNA polymerase binding surface; other site 387092000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 387092000017 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092000018 Mg2+ binding site [ion binding]; other site 387092000019 G-X-G motif; other site 387092000020 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 387092000021 anchoring element; other site 387092000022 dimer interface [polypeptide binding]; other site 387092000023 ATP binding site [chemical binding]; other site 387092000024 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 387092000025 active site 387092000026 putative metal-binding site [ion binding]; other site 387092000027 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 387092000028 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000029 metal binding site [ion binding]; metal-binding site 387092000030 active site 387092000031 I-site; other site 387092000032 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 387092000033 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 387092000034 L-aspartate oxidase; Provisional; Region: PRK06175 387092000035 succinate dehydrogenase or fumarate reductase, flavoprotein subunitGram-negative/mitochondrial subgroup; Region: sdhA_frdA_Gneg; TIGR01812 387092000036 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 387092000037 PAS domain S-box; Region: sensory_box; TIGR00229 387092000038 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092000039 putative active site [active] 387092000040 heme pocket [chemical binding]; other site 387092000041 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092000042 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000043 metal binding site [ion binding]; metal-binding site 387092000044 active site 387092000045 I-site; other site 387092000046 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 387092000047 circadian clock protein KaiC; Reviewed; Region: PRK09302 387092000048 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 387092000049 Walker A motif; other site 387092000050 ATP binding site [chemical binding]; other site 387092000051 Walker B motif; other site 387092000052 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 387092000053 Walker A motif; other site 387092000054 ATP binding site [chemical binding]; other site 387092000055 Walker B motif; other site 387092000056 amino acid transporter; Region: 2A0306; TIGR00909 387092000057 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 387092000058 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 387092000059 catalytic loop [active] 387092000060 iron binding site [ion binding]; other site 387092000061 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 387092000062 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 387092000063 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 387092000064 ligand binding site [chemical binding]; other site 387092000065 flexible hinge region; other site 387092000066 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 387092000067 YfdX protein; Region: YfdX; pfam10938 387092000068 Domain of unknown function (DUF1931); Region: DUF1931; pfam09123 387092000069 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 387092000070 Protein of unknown function (DUF505); Region: DUF505; pfam04458 387092000071 peroxiredoxin; Provisional; Region: PRK13189 387092000072 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 387092000073 dimer interface [polypeptide binding]; other site 387092000074 decamer (pentamer of dimers) interface [polypeptide binding]; other site 387092000075 catalytic triad [active] 387092000076 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 387092000077 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092000078 Walker A/P-loop; other site 387092000079 ATP binding site [chemical binding]; other site 387092000080 Q-loop/lid; other site 387092000081 ABC transporter signature motif; other site 387092000082 Walker B; other site 387092000083 D-loop; other site 387092000084 H-loop/switch region; other site 387092000085 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 387092000086 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 387092000087 dimer interface [polypeptide binding]; other site 387092000088 conserved gate region; other site 387092000089 putative PBP binding loops; other site 387092000090 ABC-ATPase subunit interface; other site 387092000091 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 387092000092 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 387092000093 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 387092000094 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 387092000095 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 387092000096 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 387092000097 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 387092000098 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 387092000099 Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_c; cd01145 387092000100 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 387092000101 putative ligand binding site [chemical binding]; other site 387092000102 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 387092000103 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 387092000104 arsenical pump membrane protein; Provisional; Region: PRK15445 387092000105 transmembrane helices; other site 387092000106 Predicted permeases [General function prediction only]; Region: COG0701 387092000107 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 387092000108 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 387092000109 Low molecular weight phosphatase family; Region: LMWPc; cd00115 387092000110 active site 387092000111 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 387092000112 putative DNA binding site [nucleotide binding]; other site 387092000113 putative Zn2+ binding site [ion binding]; other site 387092000114 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09561 387092000115 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 387092000116 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 387092000117 iron-sulfur cluster [ion binding]; other site 387092000118 [2Fe-2S] cluster binding site [ion binding]; other site 387092000119 sulfur oxidation protein SoxY; Provisional; Region: PRK07474 387092000120 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 387092000121 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 387092000122 Nuclease-related domain; Region: NERD; pfam08378 387092000123 Family description; Region: UvrD_C_2; pfam13538 387092000124 Domain of unknown function (DUF309); Region: DUF309; pfam03745 387092000125 recA bacterial DNA recombination protein; Region: RecA; cl17211 387092000126 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 387092000127 NADPH bind site [chemical binding]; other site 387092000128 putative FMN binding site [chemical binding]; other site 387092000129 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 387092000130 putative FMN binding site [chemical binding]; other site 387092000131 NADPH bind site [chemical binding]; other site 387092000132 Sulphur transport; Region: Sulf_transp; pfam04143 387092000133 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 387092000134 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 387092000135 active site 387092000136 substrate-binding site [chemical binding]; other site 387092000137 metal-binding site [ion binding] 387092000138 ATP binding site [chemical binding]; other site 387092000139 Ferredoxin thioredoxin reductase catalytic beta chain; Region: FeThRed_B; pfam02943 387092000140 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 387092000141 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 387092000142 S-adenosylmethionine binding site [chemical binding]; other site 387092000143 Predicted amidohydrolase [General function prediction only]; Region: COG0388 387092000144 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 387092000145 active site 387092000146 catalytic triad [active] 387092000147 dimer interface [polypeptide binding]; other site 387092000148 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 387092000149 dimer interface [polypeptide binding]; other site 387092000150 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 387092000151 putative radical transfer pathway; other site 387092000152 diiron center [ion binding]; other site 387092000153 tyrosyl radical; other site 387092000154 Probable gene remnant. Similar to the C-terminal region of Corynebacterium glutamicum ATCC 13032 conserved hypothetical protein (211 aa) TR:Q46063 387092000155 short chain dehydrogenase; Provisional; Region: PRK05993 387092000156 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 387092000157 NADP binding site [chemical binding]; other site 387092000158 active site 387092000159 steroid binding site; other site 387092000160 methionine sulfoxide reductase B; Provisional; Region: PRK00222 387092000161 SelR domain; Region: SelR; pfam01641 387092000162 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 387092000163 putative ADP-ribose binding site [chemical binding]; other site 387092000164 putative active site [active] 387092000165 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 387092000166 ATP cone domain; Region: ATP-cone; pfam03477 387092000167 Class I ribonucleotide reductase; Region: RNR_I; cd01679 387092000168 active site 387092000169 dimer interface [polypeptide binding]; other site 387092000170 catalytic residues [active] 387092000171 effector binding site; other site 387092000172 R2 peptide binding site; other site 387092000173 adenylosuccinate lyase; Provisional; Region: PRK08470 387092000174 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 387092000175 tetramer interface [polypeptide binding]; other site 387092000176 active site 387092000177 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 387092000178 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 387092000179 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 387092000180 active site 387092000181 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 387092000182 D-Lactate and related Dehydrogenase like proteins, NAD-binding and catalytic domains; Region: LDH_like_1; cd12187 387092000183 ligand binding site [chemical binding]; other site 387092000184 NAD binding site [chemical binding]; other site 387092000185 homodimer interface [polypeptide binding]; other site 387092000186 catalytic site [active] 387092000187 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 387092000188 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 387092000189 FeS/SAM binding site; other site 387092000190 Phosphorylase superfamily; Region: PNP_UDP_1; pfam01048 387092000191 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 387092000192 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 387092000193 substrate binding site [chemical binding]; other site 387092000194 glutamase interaction surface [polypeptide binding]; other site 387092000195 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 387092000196 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 387092000197 minor groove reading motif; other site 387092000198 helix-hairpin-helix signature motif; other site 387092000199 substrate binding pocket [chemical binding]; other site 387092000200 active site 387092000201 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 387092000202 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 387092000203 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 387092000204 S-adenosylmethionine binding site [chemical binding]; other site 387092000205 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 387092000206 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 387092000207 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 387092000208 KpsF/GutQ family protein; Region: kpsF; TIGR00393 387092000209 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 387092000210 putative active site [active] 387092000211 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 387092000212 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 387092000213 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 387092000214 RNA binding surface [nucleotide binding]; other site 387092000215 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 387092000216 active site 387092000217 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 387092000218 recombination factor protein RarA; Reviewed; Region: PRK13342 387092000219 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 387092000220 Walker A motif; other site 387092000221 ATP binding site [chemical binding]; other site 387092000222 Walker B motif; other site 387092000223 arginine finger; other site 387092000224 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 387092000225 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 387092000226 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 387092000227 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 387092000228 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 387092000229 putative active site [active] 387092000230 dimerization interface [polypeptide binding]; other site 387092000231 putative tRNAtyr binding site [nucleotide binding]; other site 387092000232 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 387092000233 active site 387092000234 MarC family integral membrane protein; Region: MarC; cl00919 387092000235 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 387092000236 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 387092000237 Outer membrane efflux protein; Region: OEP; pfam02321 387092000238 Outer membrane efflux protein; Region: OEP; pfam02321 387092000239 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 387092000240 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 387092000241 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092000242 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 387092000243 Protein export membrane protein; Region: SecD_SecF; cl14618 387092000244 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 387092000245 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 387092000246 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 387092000247 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 387092000248 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 387092000249 catalytic residues [active] 387092000250 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 387092000251 active site residue [active] 387092000252 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 387092000253 active site residue [active] 387092000254 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 387092000255 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 387092000256 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 387092000257 Cl- selectivity filter; other site 387092000258 Cl- binding residues [ion binding]; other site 387092000259 pore gating glutamate residue; other site 387092000260 dimer interface [polypeptide binding]; other site 387092000261 4Fe-4S binding domain; Region: Fer4; cl02805 387092000262 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 387092000263 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 387092000264 FAD binding pocket [chemical binding]; other site 387092000265 conserved FAD binding motif [chemical binding]; other site 387092000266 phosphate binding motif [ion binding]; other site 387092000267 beta-alpha-beta structure motif; other site 387092000268 NAD binding pocket [chemical binding]; other site 387092000269 Ion channel; Region: Ion_trans_2; pfam07885 387092000270 Ion transport protein; Region: Ion_trans; pfam00520 387092000271 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 387092000272 TrkA-N domain; Region: TrkA_N; pfam02254 387092000273 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 387092000274 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 387092000275 ligand binding site [chemical binding]; other site 387092000276 flexible hinge region; other site 387092000277 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 387092000278 heme-binding site [chemical binding]; other site 387092000279 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 387092000280 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 387092000281 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 387092000282 G1 box; other site 387092000283 GTP/Mg2+ binding site [chemical binding]; other site 387092000284 Switch I region; other site 387092000285 G2 box; other site 387092000286 G3 box; other site 387092000287 Switch II region; other site 387092000288 G4 box; other site 387092000289 G5 box; other site 387092000290 Nucleoside recognition; Region: Gate; pfam07670 387092000291 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 387092000292 Nucleoside recognition; Region: Gate; pfam07670 387092000293 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 387092000294 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 387092000295 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 387092000296 Uncharacterized conserved protein [Function unknown]; Region: COG1434 387092000297 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 387092000298 putative active site [active] 387092000299 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 387092000300 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 387092000301 dimerization interface [polypeptide binding]; other site 387092000302 putative ATP binding site [chemical binding]; other site 387092000303 spermidine synthase; Provisional; Region: PRK00811 387092000304 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 387092000305 S-adenosylmethionine binding site [chemical binding]; other site 387092000306 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 387092000307 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 387092000308 CoA-binding site [chemical binding]; other site 387092000309 ATP-binding [chemical binding]; other site 387092000310 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 387092000311 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 387092000312 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 387092000313 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl17361 387092000314 peptide chain release factor 1; Validated; Region: prfA; PRK00591 387092000315 This domain is found in peptide chain release factors; Region: PCRF; smart00937 387092000316 RF-1 domain; Region: RF-1; pfam00472 387092000317 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 387092000318 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 387092000319 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 387092000320 active site 387092000321 substrate binding site [chemical binding]; other site 387092000322 metal binding site [ion binding]; metal-binding site 387092000323 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 387092000324 lipoprotein signal peptidase; Provisional; Region: PRK14787 387092000325 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 387092000326 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 387092000327 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 387092000328 active site 387092000329 dimer interface [polypeptide binding]; other site 387092000330 motif 1; other site 387092000331 motif 2; other site 387092000332 motif 3; other site 387092000333 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 387092000334 anticodon binding site; other site 387092000335 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 387092000336 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 387092000337 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 387092000338 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 387092000339 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 387092000340 23S rRNA binding site [nucleotide binding]; other site 387092000341 L21 binding site [polypeptide binding]; other site 387092000342 L13 binding site [polypeptide binding]; other site 387092000343 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 387092000344 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 387092000345 Walker A/P-loop; other site 387092000346 ATP binding site [chemical binding]; other site 387092000347 Q-loop/lid; other site 387092000348 ABC transporter signature motif; other site 387092000349 Walker B; other site 387092000350 D-loop; other site 387092000351 H-loop/switch region; other site 387092000352 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 387092000353 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 387092000354 FtsX-like permease family; Region: FtsX; pfam02687 387092000355 Pseudogene. Similar to secretion protein HlyD. This CDS appears to have a frameshift mutation following codon 201. 387092000356 Probable gene remnant. Similar to the C-terminal region of Thiomicrospira denitrificans ATCC 33889 secretion protein HlyD (381 aa) Tmden_1362. 387092000357 Probable gene remnant. Similar to the N-terminal region of Thiomicrospira denitrificans ATCC 33889 secretion protein HlyD (381 aa) Tmden_1362. 387092000358 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 387092000359 Probable gene remnant. Similar to Pelodictyon luteolum DSM 273 cytochrome C (167 aa) Plut_1674. 387092000360 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092000361 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 387092000362 dimer interface [polypeptide binding]; other site 387092000363 phosphorylation site [posttranslational modification] 387092000364 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092000365 ATP binding site [chemical binding]; other site 387092000366 Mg2+ binding site [ion binding]; other site 387092000367 G-X-G motif; other site 387092000368 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092000369 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092000370 active site 387092000371 phosphorylation site [posttranslational modification] 387092000372 intermolecular recognition site; other site 387092000373 dimerization interface [polypeptide binding]; other site 387092000374 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 387092000375 DNA binding site [nucleotide binding] 387092000376 Fe-S metabolism associated domain; Region: SufE; cl00951 387092000377 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000378 metal binding site [ion binding]; metal-binding site 387092000379 active site 387092000380 I-site; other site 387092000381 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 387092000382 NAD-dependent deacetylase; Provisional; Region: PRK00481 387092000383 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 387092000384 Ferritin-CCC1, N-terminal ferritin-like diiron-binding domain; Region: Ferritin_CCC1_N; cd01044 387092000385 diiron binding motif [ion binding]; other site 387092000386 CCC1-related domain of ferritin; Region: Ferritin_CCC1_C; cd02431 387092000387 NnrS protein; Region: NnrS; pfam05940 387092000388 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 387092000389 RNA binding site [nucleotide binding]; other site 387092000390 ribosome small subunit-dependent GTPase A; Region: TIGR00157 387092000391 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 387092000392 GTPase/Zn-binding domain interface [polypeptide binding]; other site 387092000393 GTP/Mg2+ binding site [chemical binding]; other site 387092000394 G4 box; other site 387092000395 G5 box; other site 387092000396 G1 box; other site 387092000397 Switch I region; other site 387092000398 G2 box; other site 387092000399 G3 box; other site 387092000400 Switch II region; other site 387092000401 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 387092000402 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 387092000403 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 387092000404 active site 387092000405 metal binding site [ion binding]; metal-binding site 387092000406 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 387092000407 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 387092000408 putative ligand binding site [chemical binding]; other site 387092000409 putative NAD binding site [chemical binding]; other site 387092000410 catalytic site [active] 387092000411 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 387092000412 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 387092000413 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387092000414 ATP-grasp domain; Region: ATP-grasp; pfam02222 387092000415 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 387092000416 S-adenosylmethionine binding site [chemical binding]; other site 387092000417 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 387092000418 Domain of unknown function DUF302; Region: DUF302; cl01364 387092000419 PAS domain; Region: PAS_9; pfam13426 387092000420 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092000421 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000422 metal binding site [ion binding]; metal-binding site 387092000423 active site 387092000424 I-site; other site 387092000425 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 387092000426 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 387092000427 PAS domain S-box; Region: sensory_box; TIGR00229 387092000428 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092000429 putative active site [active] 387092000430 heme pocket [chemical binding]; other site 387092000431 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 387092000432 GAF domain; Region: GAF; pfam01590 387092000433 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092000434 PAS domain; Region: PAS_9; pfam13426 387092000435 putative active site [active] 387092000436 heme pocket [chemical binding]; other site 387092000437 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092000438 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000439 metal binding site [ion binding]; metal-binding site 387092000440 active site 387092000441 I-site; other site 387092000442 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 387092000443 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 387092000444 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 387092000445 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 387092000446 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 387092000447 active site 387092000448 NTP binding site [chemical binding]; other site 387092000449 metal binding triad [ion binding]; metal-binding site 387092000450 antibiotic binding site [chemical binding]; other site 387092000451 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 387092000452 Haemolytic domain; Region: Haemolytic; cl00506 387092000453 Cytochrome c; Region: Cytochrom_C; pfam00034 387092000454 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 387092000455 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 387092000456 active site 387092000457 catalytic tetrad [active] 387092000458 multiple promoter invertase; Provisional; Region: mpi; PRK13413 387092000459 Resolvase, N terminal domain; Region: Resolvase; smart00857 387092000460 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 387092000461 DNA-binding interface [nucleotide binding]; DNA binding site 387092000462 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 387092000463 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 387092000464 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 387092000465 Uncharacterized conserved protein [Function unknown]; Region: COG1433 387092000466 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 387092000467 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 387092000468 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 387092000469 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 387092000470 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 387092000471 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 387092000472 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 387092000473 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000474 metal binding site [ion binding]; metal-binding site 387092000475 active site 387092000476 I-site; other site 387092000477 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 387092000478 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 387092000479 active site residue [active] 387092000480 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 387092000481 TOBE domain; Region: TOBE; pfam03459 387092000482 Protein of unknown function DUF45; Region: DUF45; pfam01863 387092000483 Protein of unknown function, DUF481; Region: DUF481; pfam04338 387092000484 CTP synthetase; Validated; Region: pyrG; PRK05380 387092000485 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 387092000486 Catalytic site [active] 387092000487 active site 387092000488 UTP binding site [chemical binding]; other site 387092000489 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 387092000490 active site 387092000491 putative oxyanion hole; other site 387092000492 catalytic triad [active] 387092000493 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 387092000494 DHH family; Region: DHH; pfam01368 387092000495 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 387092000496 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 387092000497 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 387092000498 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 387092000499 NifU-like domain; Region: NifU; pfam01106 387092000500 PAS domain; Region: PAS; smart00091 387092000501 PAS domain; Region: PAS_9; pfam13426 387092000502 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092000503 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000504 metal binding site [ion binding]; metal-binding site 387092000505 active site 387092000506 I-site; other site 387092000507 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 387092000508 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 387092000509 homodecamer interface [polypeptide binding]; other site 387092000510 GTP cyclohydrolase I; Provisional; Region: PLN03044 387092000511 active site 387092000512 putative catalytic site residues [active] 387092000513 zinc binding site [ion binding]; other site 387092000514 GTP-CH-I/GFRP interaction surface; other site 387092000515 trigger factor; Provisional; Region: tig; PRK01490 387092000516 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 387092000517 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 387092000518 Clp protease; Region: CLP_protease; pfam00574 387092000519 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 387092000520 oligomer interface [polypeptide binding]; other site 387092000521 active site residues [active] 387092000522 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 387092000523 active site 387092000524 catalytic residues [active] 387092000525 metal binding site [ion binding]; metal-binding site 387092000526 Pseudogene. Similar to Mg chelatase-related protein. This CDS appears to have a frameshift mutation following codon 62. 387092000527 Probable gene remnant. Similar to the N-terminal region of Thiomicrospira denitrificans ATCC 33889 Mg chelatase-related protein (503 aa) Tmden_2033. 387092000528 Probable gene remnant. Similar to the C-terminal region of Thiomicrospira denitrificans ATCC 33889 Mg chelatase-related protein (503 aa) Tmden_2033. 387092000529 Predicted membrane protein [Function unknown]; Region: COG2855 387092000530 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 387092000531 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 387092000532 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 387092000533 putative dimerization interface [polypeptide binding]; other site 387092000534 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 387092000535 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 387092000536 putative substrate binding site [chemical binding]; other site 387092000537 putative ATP binding site [chemical binding]; other site 387092000538 Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]; Region: PurN; COG0299 387092000539 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 387092000540 active site 387092000541 substrate binding site [chemical binding]; other site 387092000542 cosubstrate binding site; other site 387092000543 catalytic site [active] 387092000544 Predicted membrane protein [Function unknown]; Region: COG3174 387092000545 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 387092000546 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 387092000547 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 387092000548 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 387092000549 ThiS interaction site; other site 387092000550 putative active site [active] 387092000551 tetramer interface [polypeptide binding]; other site 387092000552 Ion channel; Region: Ion_trans_2; pfam07885 387092000553 TrkA-N domain; Region: TrkA_N; pfam02254 387092000554 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 387092000555 TrkA-C domain; Region: TrkA_C; pfam02080 387092000556 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 387092000557 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 387092000558 catalytic residues [active] 387092000559 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 387092000560 Na2 binding site [ion binding]; other site 387092000561 putative substrate binding site 1 [chemical binding]; other site 387092000562 Na binding site 1 [ion binding]; other site 387092000563 putative substrate binding site 2 [chemical binding]; other site 387092000564 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 387092000565 active site 387092000566 oxyanion hole [active] 387092000567 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 387092000568 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 387092000569 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 387092000570 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 387092000571 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 387092000572 DXD motif; other site 387092000573 Cellulose synthase-like protein; Region: PLN02893 387092000574 Tetratricopeptide repeat; Region: TPR_15; pfam13429 387092000575 Alginate lyase; Region: Alginate_lyase2; pfam08787 387092000576 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 387092000577 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 387092000578 Right handed beta helix region; Region: Beta_helix; pfam13229 387092000579 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 387092000580 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 387092000581 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 387092000582 active site 387092000583 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 387092000584 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 387092000585 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 387092000586 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 387092000587 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 387092000588 active site 387092000589 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 387092000590 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 387092000591 phosphopeptide binding site; other site 387092000592 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 387092000593 Catalytic domain of Protein Kinases; Region: PKc; cd00180 387092000594 active site 387092000595 ATP binding site [chemical binding]; other site 387092000596 substrate binding site [chemical binding]; other site 387092000597 activation loop (A-loop); other site 387092000598 FOG: WD40 repeat [General function prediction only]; Region: COG2319 387092000599 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cd00200 387092000600 structural tetrad; other site 387092000601 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 387092000602 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 387092000603 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 387092000604 Substrate binding site; other site 387092000605 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 387092000606 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000607 metal binding site [ion binding]; metal-binding site 387092000608 active site 387092000609 I-site; other site 387092000610 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 387092000611 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 387092000612 FAD dependent oxidoreductase; Region: DAO; pfam01266 387092000613 phosphoglycolate phosphatase; Provisional; Region: PRK13222 387092000614 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 387092000615 motif I; other site 387092000616 active site 387092000617 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 387092000618 motif II; other site 387092000619 Family of unknown function (DUF490); Region: DUF490; pfam04357 387092000620 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 387092000621 Surface antigen; Region: Bac_surface_Ag; pfam01103 387092000622 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3787; cl17897 387092000623 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 387092000624 The CHAD domain is an alpha-helical domain functionally associated with some members of the adenylate cyclase family; Region: CHAD; smart00880 387092000625 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 387092000626 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 387092000627 minor groove reading motif; other site 387092000628 helix-hairpin-helix signature motif; other site 387092000629 substrate binding pocket [chemical binding]; other site 387092000630 active site 387092000631 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 387092000632 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 387092000633 Uncharacterized conserved protein (DUF2267); Region: DUF2267; pfam10025 387092000634 Hemerythrin; Region: Hemerythrin; cd12107 387092000635 Fe binding site [ion binding]; other site 387092000636 PAS domain S-box; Region: sensory_box; TIGR00229 387092000637 PAS domain; Region: PAS; smart00091 387092000638 putative active site [active] 387092000639 heme pocket [chemical binding]; other site 387092000640 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092000641 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000642 metal binding site [ion binding]; metal-binding site 387092000643 active site 387092000644 I-site; other site 387092000645 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 387092000646 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 387092000647 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 387092000648 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 387092000649 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 387092000650 Ligand Binding Site [chemical binding]; other site 387092000651 DNA primase; Validated; Region: dnaG; PRK05667 387092000652 CHC2 zinc finger; Region: zf-CHC2; pfam01807 387092000653 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 387092000654 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 387092000655 active site 387092000656 metal binding site [ion binding]; metal-binding site 387092000657 interdomain interaction site; other site 387092000658 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 387092000659 binding surface 387092000660 Tetratricopeptide repeat; Region: TPR_12; pfam13424 387092000661 TPR motif; other site 387092000662 Tetratricopeptide repeat; Region: TPR_16; pfam13432 387092000663 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 387092000664 RNA/DNA hybrid binding site [nucleotide binding]; other site 387092000665 active site 387092000666 ribonuclease III; Reviewed; Region: rnc; PRK00102 387092000667 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 387092000668 dimerization interface [polypeptide binding]; other site 387092000669 active site 387092000670 metal binding site [ion binding]; metal-binding site 387092000671 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 387092000672 dsRNA binding site [nucleotide binding]; other site 387092000673 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 387092000674 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 387092000675 Tetramer interface [polypeptide binding]; other site 387092000676 active site 387092000677 FMN-binding site [chemical binding]; other site 387092000678 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 387092000679 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 387092000680 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 387092000681 RNA/DNA hybrid binding site [nucleotide binding]; other site 387092000682 active site 387092000683 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 387092000684 PIN domain of the VapC-like Sll0205 protein and homologs; Region: PIN_Sll0205; cd09872 387092000685 putative active site [active] 387092000686 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 387092000687 AAA domain; Region: AAA_14; pfam13173 387092000688 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 387092000689 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 387092000690 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 387092000691 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 387092000692 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 387092000693 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 387092000694 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 387092000695 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 387092000696 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 387092000697 putative translocon binding site; other site 387092000698 protein-rRNA interface [nucleotide binding]; other site 387092000699 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 387092000700 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 387092000701 G-X-X-G motif; other site 387092000702 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 387092000703 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 387092000704 23S rRNA interface [nucleotide binding]; other site 387092000705 5S rRNA interface [nucleotide binding]; other site 387092000706 putative antibiotic binding site [chemical binding]; other site 387092000707 L25 interface [polypeptide binding]; other site 387092000708 L27 interface [polypeptide binding]; other site 387092000709 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 387092000710 L23 interface [polypeptide binding]; other site 387092000711 signal recognition particle (SRP54) interaction site; other site 387092000712 trigger factor interaction site; other site 387092000713 23S rRNA interface [nucleotide binding]; other site 387092000714 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 387092000715 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 387092000716 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 387092000717 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 387092000718 RNA binding site [nucleotide binding]; other site 387092000719 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 387092000720 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 387092000721 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 387092000722 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 387092000723 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 387092000724 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 387092000725 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 387092000726 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 387092000727 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 387092000728 23S rRNA interface [nucleotide binding]; other site 387092000729 5S rRNA interface [nucleotide binding]; other site 387092000730 L27 interface [polypeptide binding]; other site 387092000731 L5 interface [polypeptide binding]; other site 387092000732 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 387092000733 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 387092000734 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 387092000735 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 387092000736 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 387092000737 SecY translocase; Region: SecY; pfam00344 387092000738 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 387092000739 active site 387092000740 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 387092000741 rRNA binding site [nucleotide binding]; other site 387092000742 predicted 30S ribosome binding site; other site 387092000743 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 387092000744 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 387092000745 30S ribosomal protein S13; Region: bact_S13; TIGR03631 387092000746 30S ribosomal protein S11; Validated; Region: PRK05309 387092000747 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 387092000748 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 387092000749 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 387092000750 RNA binding surface [nucleotide binding]; other site 387092000751 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 387092000752 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 387092000753 alphaNTD homodimer interface [polypeptide binding]; other site 387092000754 alphaNTD - beta interaction site [polypeptide binding]; other site 387092000755 alphaNTD - beta' interaction site [polypeptide binding]; other site 387092000756 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 387092000757 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 387092000758 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 387092000759 TPR repeat; Region: TPR_11; pfam13414 387092000760 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 387092000761 binding surface 387092000762 TPR motif; other site 387092000763 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 387092000764 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 387092000765 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 387092000766 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 387092000767 dimer interface [polypeptide binding]; other site 387092000768 [2Fe-2S] cluster binding site [ion binding]; other site 387092000769 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 387092000770 tetramerization interface [polypeptide binding]; other site 387092000771 active site 387092000772 hypothetical protein; Provisional; Region: PRK03762 387092000773 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 387092000774 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 387092000775 substrate binding pocket [chemical binding]; other site 387092000776 chain length determination region; other site 387092000777 substrate-Mg2+ binding site; other site 387092000778 catalytic residues [active] 387092000779 aspartate-rich region 1; other site 387092000780 active site lid residues [active] 387092000781 aspartate-rich region 2; other site 387092000782 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 387092000783 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 387092000784 TPP-binding site [chemical binding]; other site 387092000785 dimer interface [polypeptide binding]; other site 387092000786 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 387092000787 PYR/PP interface [polypeptide binding]; other site 387092000788 dimer interface [polypeptide binding]; other site 387092000789 TPP binding site [chemical binding]; other site 387092000790 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 387092000791 Helix-turn-helix domain; Region: HTH_28; pfam13518 387092000792 putative transposase OrfB; Reviewed; Region: PHA02517 387092000793 Homeodomain-like domain; Region: HTH_32; pfam13565 387092000794 Integrase core domain; Region: rve; pfam00665 387092000795 Integrase core domain; Region: rve_3; pfam13683 387092000796 elongation factor Tu; Reviewed; Region: PRK00049 387092000797 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 387092000798 G1 box; other site 387092000799 GEF interaction site [polypeptide binding]; other site 387092000800 GTP/Mg2+ binding site [chemical binding]; other site 387092000801 Switch I region; other site 387092000802 G2 box; other site 387092000803 G3 box; other site 387092000804 Switch II region; other site 387092000805 G4 box; other site 387092000806 G5 box; other site 387092000807 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 387092000808 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 387092000809 Antibiotic Binding Site [chemical binding]; other site 387092000810 50S ribosomal protein L33; Validated; Region: rpmG; PRK00504 387092000811 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 387092000812 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 387092000813 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 387092000814 putative homodimer interface [polypeptide binding]; other site 387092000815 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 387092000816 heterodimer interface [polypeptide binding]; other site 387092000817 homodimer interface [polypeptide binding]; other site 387092000818 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 387092000819 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 387092000820 23S rRNA interface [nucleotide binding]; other site 387092000821 L7/L12 interface [polypeptide binding]; other site 387092000822 putative thiostrepton binding site; other site 387092000823 L25 interface [polypeptide binding]; other site 387092000824 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 387092000825 mRNA/rRNA interface [nucleotide binding]; other site 387092000826 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 387092000827 23S rRNA interface [nucleotide binding]; other site 387092000828 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 387092000829 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 387092000830 L11 interface [polypeptide binding]; other site 387092000831 putative EF-Tu interaction site [polypeptide binding]; other site 387092000832 putative EF-G interaction site [polypeptide binding]; other site 387092000833 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 387092000834 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 387092000835 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 387092000836 RPB11 interaction site [polypeptide binding]; other site 387092000837 RPB12 interaction site [polypeptide binding]; other site 387092000838 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 387092000839 RPB3 interaction site [polypeptide binding]; other site 387092000840 RPB1 interaction site [polypeptide binding]; other site 387092000841 RPB11 interaction site [polypeptide binding]; other site 387092000842 RPB10 interaction site [polypeptide binding]; other site 387092000843 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 387092000844 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 387092000845 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 387092000846 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 387092000847 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 387092000848 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 387092000849 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 387092000850 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 387092000851 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 387092000852 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 387092000853 DNA binding site [nucleotide binding] 387092000854 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 387092000855 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 387092000856 S17 interaction site [polypeptide binding]; other site 387092000857 S8 interaction site; other site 387092000858 16S rRNA interaction site [nucleotide binding]; other site 387092000859 streptomycin interaction site [chemical binding]; other site 387092000860 23S rRNA interaction site [nucleotide binding]; other site 387092000861 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 387092000862 30S ribosomal protein S7; Validated; Region: PRK05302 387092000863 elongation factor G; Reviewed; Region: PRK00007 387092000864 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 387092000865 G1 box; other site 387092000866 putative GEF interaction site [polypeptide binding]; other site 387092000867 GTP/Mg2+ binding site [chemical binding]; other site 387092000868 Switch I region; other site 387092000869 G2 box; other site 387092000870 G3 box; other site 387092000871 Switch II region; other site 387092000872 G4 box; other site 387092000873 G5 box; other site 387092000874 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 387092000875 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 387092000876 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 387092000877 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 387092000878 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092000879 active site 387092000880 phosphorylation site [posttranslational modification] 387092000881 intermolecular recognition site; other site 387092000882 dimerization interface [polypeptide binding]; other site 387092000883 CheB methylesterase; Region: CheB_methylest; pfam01339 387092000884 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 387092000885 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 387092000886 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 387092000887 CheW-like domain; Region: CheW; pfam01584 387092000888 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 387092000889 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 387092000890 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092000891 dimer interface [polypeptide binding]; other site 387092000892 putative CheW interface [polypeptide binding]; other site 387092000893 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 387092000894 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 387092000895 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 387092000896 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 387092000897 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 387092000898 active site 387092000899 DNA binding site [nucleotide binding] 387092000900 Predicted transcriptional regulator [Transcription]; Region: COG2932 387092000901 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 387092000902 Catalytic site [active] 387092000903 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 387092000904 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 387092000905 active site 387092000906 metal binding site [ion binding]; metal-binding site 387092000907 Uncharacterized conserved protein [Function unknown]; Region: COG1656 387092000908 Protein of unknown function DUF82; Region: DUF82; pfam01927 387092000909 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 387092000910 prephenate dehydrogenase; Validated; Region: PRK08507 387092000911 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 387092000912 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 387092000913 endonuclease IV; Provisional; Region: PRK01060 387092000914 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 387092000915 AP (apurinic/apyrimidinic) site pocket; other site 387092000916 DNA interaction; other site 387092000917 Metal-binding active site; metal-binding site 387092000918 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 387092000919 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 387092000920 Walker A motif; other site 387092000921 ATP binding site [chemical binding]; other site 387092000922 Walker B motif; other site 387092000923 arginine finger; other site 387092000924 NADH dehydrogenase subunit A; Validated; Region: PRK08489 387092000925 NADH dehydrogenase subunit B; Validated; Region: PRK06411 387092000926 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 387092000927 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 387092000928 NADH dehydrogenase subunit D; Validated; Region: PRK06075 387092000929 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 387092000930 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 387092000931 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 387092000932 NADH dehydrogenase subunit G; Validated; Region: PRK08493 387092000933 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 387092000934 catalytic loop [active] 387092000935 iron binding site [ion binding]; other site 387092000936 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 387092000937 4Fe-4S binding domain; Region: Fer4; pfam00037 387092000938 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 387092000939 molybdopterin cofactor binding site; other site 387092000940 NADH dehydrogenase subunit G; Validated; Region: PRK08493 387092000941 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 387092000942 catalytic loop [active] 387092000943 iron binding site [ion binding]; other site 387092000944 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 387092000945 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 387092000946 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 387092000947 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 387092000948 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 387092000949 4Fe-4S binding domain; Region: Fer4; cl02805 387092000950 4Fe-4S binding domain; Region: Fer4; pfam00037 387092000951 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 387092000952 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 387092000953 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 387092000954 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 387092000955 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 387092000956 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 387092000957 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 387092000958 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 387092000959 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 387092000960 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 387092000961 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 387092000962 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 387092000963 prenyltransferase; Reviewed; Region: ubiA; PRK12874 387092000964 UbiA prenyltransferase family; Region: UbiA; pfam01040 387092000965 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092000966 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092000967 metal binding site [ion binding]; metal-binding site 387092000968 active site 387092000969 I-site; other site 387092000970 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 387092000971 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 387092000972 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 387092000973 active site clefts [active] 387092000974 zinc binding site [ion binding]; other site 387092000975 dimer interface [polypeptide binding]; other site 387092000976 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 387092000977 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 387092000978 Sulfate transporter family; Region: Sulfate_transp; pfam00916 387092000979 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 387092000980 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 387092000981 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 387092000982 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 387092000983 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 387092000984 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 387092000985 Mg++ binding site [ion binding]; other site 387092000986 putative catalytic motif [active] 387092000987 putative substrate binding site [chemical binding]; other site 387092000988 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 387092000989 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 387092000990 NAD(P) binding site [chemical binding]; other site 387092000991 homotetramer interface [polypeptide binding]; other site 387092000992 homodimer interface [polypeptide binding]; other site 387092000993 active site 387092000994 acyl carrier protein; Provisional; Region: acpP; PRK00982 387092000995 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 387092000996 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 387092000997 dimer interface [polypeptide binding]; other site 387092000998 active site 387092000999 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 387092001000 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 387092001001 Protein of unknown function (DUF465); Region: DUF465; cl01070 387092001002 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 387092001003 heterotetramer interface [polypeptide binding]; other site 387092001004 active site pocket [active] 387092001005 cleavage site 387092001006 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 387092001007 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 387092001008 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 387092001009 substrate binding site [chemical binding]; other site 387092001010 hexamer interface [polypeptide binding]; other site 387092001011 metal binding site [ion binding]; metal-binding site 387092001012 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 387092001013 active site 387092001014 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 387092001015 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 387092001016 active site 387092001017 catalytic site [active] 387092001018 substrate binding site [chemical binding]; other site 387092001019 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 387092001020 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 387092001021 Polypeptide deformylase; Region: Pep_deformylase; pfam01327 387092001022 active site 387092001023 catalytic residues [active] 387092001024 metal binding site [ion binding]; metal-binding site 387092001025 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 387092001026 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 387092001027 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 387092001028 trimer interface [polypeptide binding]; other site 387092001029 putative metal binding site [ion binding]; other site 387092001030 polyphosphate kinase; Provisional; Region: PRK05443 387092001031 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 387092001032 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 387092001033 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 387092001034 putative domain interface [polypeptide binding]; other site 387092001035 putative active site [active] 387092001036 catalytic site [active] 387092001037 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 387092001038 putative domain interface [polypeptide binding]; other site 387092001039 putative active site [active] 387092001040 catalytic site [active] 387092001041 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 387092001042 active site clefts [active] 387092001043 zinc binding site [ion binding]; other site 387092001044 dimer interface [polypeptide binding]; other site 387092001045 excinuclease ABC subunit B; Provisional; Region: PRK05298 387092001046 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 387092001047 ATP binding site [chemical binding]; other site 387092001048 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 387092001049 nucleotide binding region [chemical binding]; other site 387092001050 ATP-binding site [chemical binding]; other site 387092001051 Ultra-violet resistance protein B; Region: UvrB; pfam12344 387092001052 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 387092001053 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 387092001054 primosome assembly protein PriA; Validated; Region: PRK05580 387092001055 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 387092001056 ATP binding site [chemical binding]; other site 387092001057 putative Mg++ binding site [ion binding]; other site 387092001058 helicase superfamily c-terminal domain; Region: HELICc; smart00490 387092001059 ATP-binding site [chemical binding]; other site 387092001060 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 387092001061 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 387092001062 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 387092001063 replicative DNA helicase; Provisional; Region: PRK08506 387092001064 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 387092001065 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 387092001066 Walker A motif; other site 387092001067 ATP binding site [chemical binding]; other site 387092001068 Walker B motif; other site 387092001069 DNA binding loops [nucleotide binding] 387092001070 Competence protein; Region: Competence; pfam03772 387092001071 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 387092001072 FAD binding domain; Region: FAD_binding_4; pfam01565 387092001073 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 387092001074 putative peptidase; Provisional; Region: PRK11649 387092001075 Peptidase family M23; Region: Peptidase_M23; pfam01551 387092001076 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 387092001077 MgtE intracellular N domain; Region: MgtE_N; smart00924 387092001078 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 387092001079 Divalent cation transporter; Region: MgtE; pfam01769 387092001080 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 387092001081 dimer interface [polypeptide binding]; other site 387092001082 ADP-ribose binding site [chemical binding]; other site 387092001083 active site 387092001084 nudix motif; other site 387092001085 metal binding site [ion binding]; metal-binding site 387092001086 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 387092001087 heme-binding site [chemical binding]; other site 387092001088 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 387092001089 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 387092001090 putative active site; other site 387092001091 catalytic triad [active] 387092001092 putative dimer interface [polypeptide binding]; other site 387092001093 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 387092001094 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 387092001095 ABC-ATPase subunit interface; other site 387092001096 dimer interface [polypeptide binding]; other site 387092001097 putative PBP binding regions; other site 387092001098 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 387092001099 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 387092001100 Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding...; Region: ZntC; cd01018 387092001101 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 387092001102 putative metal binding residues [ion binding]; other site 387092001103 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 387092001104 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 387092001105 Virulence-associated protein and related proteins [Function unknown]; Region: VagC; COG4456 387092001106 PemK-like protein; Region: PemK; pfam02452 387092001107 Domain of unknown function (DUF4268); Region: DUF4268; pfam14088 387092001108 alanine racemase; Reviewed; Region: alr; PRK00053 387092001109 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 387092001110 active site 387092001111 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 387092001112 dimer interface [polypeptide binding]; other site 387092001113 substrate binding site [chemical binding]; other site 387092001114 catalytic residues [active] 387092001115 Prokaryotic metallothionein; Region: Metallothio_Pro; pfam02069 387092001116 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 387092001117 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 387092001118 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 387092001119 dimerization interface [polypeptide binding]; other site 387092001120 active site 387092001121 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS; cd00384 387092001122 dimer interface [polypeptide binding]; other site 387092001123 active site 387092001124 Schiff base residues; other site 387092001125 ornithine carbamoyltransferase; Provisional; Region: PRK00779 387092001126 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 387092001127 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 387092001128 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 387092001129 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 387092001130 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 387092001131 FeS/SAM binding site; other site 387092001132 HemN C-terminal domain; Region: HemN_C; pfam06969 387092001133 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 387092001134 AAA domain; Region: AAA_30; pfam13604 387092001135 putative recombination protein RecB; Provisional; Region: PRK13909 387092001136 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 387092001137 Cysteine-rich domain; Region: CCG; pfam02754 387092001138 Cysteine-rich domain; Region: CCG; pfam02754 387092001139 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 387092001140 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 387092001141 active site 387092001142 zinc binding site [ion binding]; other site 387092001143 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092001144 dimer interface [polypeptide binding]; other site 387092001145 putative CheW interface [polypeptide binding]; other site 387092001146 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 387092001147 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 387092001148 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 387092001149 Domain of unknown function DUF20; Region: UPF0118; pfam01594 387092001150 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 387092001151 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 387092001152 Walker A motif; other site 387092001153 ATP binding site [chemical binding]; other site 387092001154 Walker B motif; other site 387092001155 arginine finger; other site 387092001156 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 387092001157 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 387092001158 oligomerization interface [polypeptide binding]; other site 387092001159 active site 387092001160 metal binding site [ion binding]; metal-binding site 387092001161 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 387092001162 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 387092001163 substrate binding site [chemical binding]; other site 387092001164 active site 387092001165 catalytic residues [active] 387092001166 heterodimer interface [polypeptide binding]; other site 387092001167 para-aminobenzoate synthase component I; Validated; Region: PRK07093 387092001168 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 387092001169 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 387092001170 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 387092001171 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 387092001172 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 387092001173 AAA domain; Region: AAA_26; pfam13500 387092001174 Uncharacterized conserved protein [Function unknown]; Region: COG2127 387092001175 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 387092001176 Clp amino terminal domain; Region: Clp_N; pfam02861 387092001177 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 387092001178 Walker A motif; other site 387092001179 ATP binding site [chemical binding]; other site 387092001180 Walker B motif; other site 387092001181 arginine finger; other site 387092001182 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 387092001183 Walker A motif; other site 387092001184 ATP binding site [chemical binding]; other site 387092001185 Walker B motif; other site 387092001186 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 387092001187 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 387092001188 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 387092001189 putative active site [active] 387092001190 transaldolase; Provisional; Region: PRK03903 387092001191 catalytic residue [active] 387092001192 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 387092001193 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 387092001194 ATP binding site [chemical binding]; other site 387092001195 Walker B motif; other site 387092001196 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 387092001197 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 387092001198 5S rRNA interface [nucleotide binding]; other site 387092001199 CTC domain interface [polypeptide binding]; other site 387092001200 L16 interface [polypeptide binding]; other site 387092001201 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 387092001202 putative active site [active] 387092001203 catalytic residue [active] 387092001204 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 387092001205 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 387092001206 diaminopimelate decarboxylase; Region: lysA; TIGR01048 387092001207 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 387092001208 active site 387092001209 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 387092001210 substrate binding site [chemical binding]; other site 387092001211 catalytic residues [active] 387092001212 dimer interface [polypeptide binding]; other site 387092001213 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 387092001214 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 387092001215 active site 387092001216 motif I; other site 387092001217 motif II; other site 387092001218 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 387092001219 Chorismate mutase type II; Region: CM_2; cl00693 387092001220 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 387092001221 Prephenate dehydratase; Region: PDT; pfam00800 387092001222 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 387092001223 putative L-Phe binding site [chemical binding]; other site 387092001224 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 387092001225 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 387092001226 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092001227 homodimer interface [polypeptide binding]; other site 387092001228 catalytic residue [active] 387092001229 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 387092001230 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 387092001231 TPP-binding site; other site 387092001232 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 387092001233 PYR/PP interface [polypeptide binding]; other site 387092001234 dimer interface [polypeptide binding]; other site 387092001235 TPP binding site [chemical binding]; other site 387092001236 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 387092001237 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 387092001238 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 387092001239 dimer interface [polypeptide binding]; other site 387092001240 decamer (pentamer of dimers) interface [polypeptide binding]; other site 387092001241 catalytic triad [active] 387092001242 peroxidatic and resolving cysteines [active] 387092001243 S-adenosylmethionine synthetase; Validated; Region: PRK05250 387092001244 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 387092001245 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 387092001246 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 387092001247 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 387092001248 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 387092001249 active site 387092001250 multimer interface [polypeptide binding]; other site 387092001251 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 387092001252 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 387092001253 putative phosphate acyltransferase; Provisional; Region: PRK05331 387092001254 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 387092001255 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 387092001256 dimer interface [polypeptide binding]; other site 387092001257 active site 387092001258 CoA binding pocket [chemical binding]; other site 387092001259 MoxR-like ATPases [General function prediction only]; Region: COG0714 387092001260 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 387092001261 Walker A motif; other site 387092001262 ATP binding site [chemical binding]; other site 387092001263 Walker B motif; other site 387092001264 arginine finger; other site 387092001265 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 387092001266 Protein of unknown function DUF58; Region: DUF58; pfam01882 387092001267 hypothetical protein; Provisional; Region: PRK13685 387092001268 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 387092001269 metal ion-dependent adhesion site (MIDAS); other site 387092001270 von Willebrand factor type A domain; Region: VWA_2; pfam13519 387092001271 metal ion-dependent adhesion site (MIDAS); other site 387092001272 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 387092001273 binding surface 387092001274 TPR motif; other site 387092001275 TPR repeat; Region: TPR_11; pfam13414 387092001276 Oxygen tolerance; Region: BatD; pfam13584 387092001277 prephenate dehydrogenase; Validated; Region: PRK08507 387092001278 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 387092001279 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 387092001280 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 387092001281 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 387092001282 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 387092001283 Surface antigen; Region: Bac_surface_Ag; pfam01103 387092001284 exopolyphosphatase; Region: exo_poly_only; TIGR03706 387092001285 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 387092001286 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 387092001287 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092001288 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 387092001289 dimer interface [polypeptide binding]; other site 387092001290 phosphorylation site [posttranslational modification] 387092001291 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092001292 ATP binding site [chemical binding]; other site 387092001293 Mg2+ binding site [ion binding]; other site 387092001294 G-X-G motif; other site 387092001295 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092001296 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092001297 active site 387092001298 phosphorylation site [posttranslational modification] 387092001299 intermolecular recognition site; other site 387092001300 dimerization interface [polypeptide binding]; other site 387092001301 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 387092001302 DNA binding site [nucleotide binding] 387092001303 Dihydroneopterin aldolase; Region: FolB; pfam02152 387092001304 active site 387092001305 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 387092001306 quinolinate synthetase; Provisional; Region: PRK09375 387092001307 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 387092001308 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 387092001309 dimerization interface [polypeptide binding]; other site 387092001310 active site 387092001311 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 387092001312 DHH family; Region: DHH; pfam01368 387092001313 DHHA1 domain; Region: DHHA1; pfam02272 387092001314 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 387092001315 Peptidase family M23; Region: Peptidase_M23; pfam01551 387092001316 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 387092001317 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 387092001318 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 387092001319 homoserine kinase; Provisional; Region: PRK01212 387092001320 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 387092001321 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 387092001322 translation initiation factor IF-2; Region: IF-2; TIGR00487 387092001323 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 387092001324 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 387092001325 G1 box; other site 387092001326 putative GEF interaction site [polypeptide binding]; other site 387092001327 GTP/Mg2+ binding site [chemical binding]; other site 387092001328 Switch I region; other site 387092001329 G2 box; other site 387092001330 G3 box; other site 387092001331 Switch II region; other site 387092001332 G4 box; other site 387092001333 G5 box; other site 387092001334 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 387092001335 Translation-initiation factor 2; Region: IF-2; pfam11987 387092001336 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 387092001337 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 387092001338 ribosome maturation protein RimP; Reviewed; Region: PRK00092 387092001339 Sm and related proteins; Region: Sm_like; cl00259 387092001340 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 387092001341 putative oligomer interface [polypeptide binding]; other site 387092001342 putative RNA binding site [nucleotide binding]; other site 387092001343 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 387092001344 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 387092001345 catalytic motif [active] 387092001346 Zn binding site [ion binding]; other site 387092001347 RibD C-terminal domain; Region: RibD_C; cl17279 387092001348 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 387092001349 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 387092001350 S-adenosylmethionine binding site [chemical binding]; other site 387092001351 Nitrate and nitrite sensing; Region: NIT; pfam08376 387092001352 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092001353 PAS domain; Region: PAS_9; pfam13426 387092001354 putative active site [active] 387092001355 heme pocket [chemical binding]; other site 387092001356 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092001357 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092001358 metal binding site [ion binding]; metal-binding site 387092001359 active site 387092001360 I-site; other site 387092001361 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 387092001362 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 387092001363 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 387092001364 generic binding surface II; other site 387092001365 generic binding surface I; other site 387092001366 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 387092001367 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 387092001368 tandem repeat interface [polypeptide binding]; other site 387092001369 oligomer interface [polypeptide binding]; other site 387092001370 active site residues [active] 387092001371 chlorohydrolase; Provisional; Region: PRK08418 387092001372 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 387092001373 active site 387092001374 Dehydroquinase class II; Region: DHquinase_II; pfam01220 387092001375 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 387092001376 trimer interface [polypeptide binding]; other site 387092001377 active site 387092001378 dimer interface [polypeptide binding]; other site 387092001379 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 387092001380 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 387092001381 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 387092001382 active site 387092001383 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 387092001384 catalytic center binding site [active] 387092001385 ATP binding site [chemical binding]; other site 387092001386 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 387092001387 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 387092001388 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 387092001389 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 387092001390 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 387092001391 Ligand Binding Site [chemical binding]; other site 387092001392 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 387092001393 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 387092001394 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 387092001395 active site 387092001396 GTP-binding protein LepA; Provisional; Region: PRK05433 387092001397 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 387092001398 G1 box; other site 387092001399 putative GEF interaction site [polypeptide binding]; other site 387092001400 GTP/Mg2+ binding site [chemical binding]; other site 387092001401 Switch I region; other site 387092001402 G2 box; other site 387092001403 G3 box; other site 387092001404 Switch II region; other site 387092001405 G4 box; other site 387092001406 G5 box; other site 387092001407 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 387092001408 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 387092001409 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 387092001410 comF family protein; Region: comF; TIGR00201 387092001411 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 387092001412 active site 387092001413 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 387092001414 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 387092001415 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 387092001416 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 387092001417 active site 387092001418 DNA binding site [nucleotide binding] 387092001419 Int/Topo IB signature motif; other site 387092001420 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea; Region: NTP-PPase_u3; cd11540 387092001421 putative metal binding site [ion binding]; other site 387092001422 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 387092001423 putative active site [active] 387092001424 DEAD-like helicases superfamily; Region: DEXDc; smart00487 387092001425 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 387092001426 single-stranded DNA-binding protein; Region: PHA00458 387092001427 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 387092001428 non-specific DNA binding site [nucleotide binding]; other site 387092001429 salt bridge; other site 387092001430 sequence-specific DNA binding site [nucleotide binding]; other site 387092001431 Predicted transcriptional regulator [Transcription]; Region: COG2932 387092001432 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 387092001433 Catalytic site [active] 387092001434 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 387092001435 Phage regulatory protein CII (CP76); Region: Phage_CP76; pfam06892 387092001436 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 387092001437 nucleotide binding site [chemical binding]; other site 387092001438 Terminase small subunit; Region: Terminase_2; pfam03592 387092001439 Phage terminase large subunit; Region: Terminase_3; cl12054 387092001440 Terminase-like family; Region: Terminase_6; pfam03237 387092001441 Mu-like prophage protein [General function prediction only]; Region: COG3941 387092001442 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 387092001443 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 387092001444 RHS Repeat; Region: RHS_repeat; cl11982 387092001445 Glycosyl hydrolase 108; Region: Glyco_hydro_108; pfam05838 387092001446 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 387092001447 Integrase core domain; Region: rve; pfam00665 387092001448 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 387092001449 Integrase core domain; Region: rve_3; pfam13683 387092001450 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 387092001451 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 387092001452 FeS/SAM binding site; other site 387092001453 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 387092001454 substrate binding site [chemical binding]; other site 387092001455 active site 387092001456 Uncharacterized protein family, UPF0114; Region: UPF0114; pfam03350 387092001457 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 387092001458 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 387092001459 DNA gyrase subunit A; Validated; Region: PRK05560 387092001460 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 387092001461 CAP-like domain; other site 387092001462 active site 387092001463 primary dimer interface [polypeptide binding]; other site 387092001464 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 387092001465 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 387092001466 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 387092001467 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 387092001468 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 387092001469 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 387092001470 AAA ATPase domain; Region: AAA_16; pfam13191 387092001471 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 387092001472 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 387092001473 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 387092001474 Nitrogen regulatory protein P-II; Region: P-II; smart00938 387092001475 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cl17355 387092001476 DNA binding site [nucleotide binding] 387092001477 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 387092001478 binding surface 387092001479 TPR motif; other site 387092001480 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 387092001481 TPR motif; other site 387092001482 Urea transporter; Region: UT; pfam03253 387092001483 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 387092001484 Peptidase family M23; Region: Peptidase_M23; pfam01551 387092001485 diaminopimelate decarboxylase; Region: lysA; TIGR01048 387092001486 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE; Region: PLPDE_III_MccE_like; cd06841 387092001487 dimer interface [polypeptide binding]; other site 387092001488 active site 387092001489 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 387092001490 catalytic residues [active] 387092001491 substrate binding site [chemical binding]; other site 387092001492 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 387092001493 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 387092001494 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 387092001495 FMN-binding domain; Region: FMN_bind; pfam04205 387092001496 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 387092001497 ApbE family; Region: ApbE; pfam02424 387092001498 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 387092001499 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 387092001500 Multicopper oxidase; Region: Cu-oxidase; pfam00394 387092001501 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 387092001502 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 387092001503 Bacterial protein of unknown function (YtfJ_HI0045); Region: YtfJ_HI0045; cl17398 387092001504 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 387092001505 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 387092001506 active site 387092001507 catalytic site [active] 387092001508 metal binding site [ion binding]; metal-binding site 387092001509 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 387092001510 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 387092001511 ring oligomerisation interface [polypeptide binding]; other site 387092001512 ATP/Mg binding site [chemical binding]; other site 387092001513 stacking interactions; other site 387092001514 hinge regions; other site 387092001515 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 387092001516 oligomerisation interface [polypeptide binding]; other site 387092001517 mobile loop; other site 387092001518 roof hairpin; other site 387092001519 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092001520 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092001521 active site 387092001522 phosphorylation site [posttranslational modification] 387092001523 intermolecular recognition site; other site 387092001524 dimerization interface [polypeptide binding]; other site 387092001525 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 387092001526 DNA binding site [nucleotide binding] 387092001527 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 387092001528 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 387092001529 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 387092001530 Histidine kinase; Region: HisKA_2; pfam07568 387092001531 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092001532 ATP binding site [chemical binding]; other site 387092001533 Mg2+ binding site [ion binding]; other site 387092001534 G-X-G motif; other site 387092001535 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 387092001536 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cd00296 387092001537 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 387092001538 active site 387092001539 dimer interface [polypeptide binding]; other site 387092001540 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]; Region: MutS; COG0249 387092001541 MutS domain I; Region: MutS_I; pfam01624 387092001542 MutS domain II; Region: MutS_II; pfam05188 387092001543 MutS domain III; Region: MutS_III; pfam05192 387092001544 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092001545 Walker A/P-loop; other site 387092001546 ATP binding site [chemical binding]; other site 387092001547 Q-loop/lid; other site 387092001548 ABC transporter signature motif; other site 387092001549 Walker B; other site 387092001550 D-loop; other site 387092001551 H-loop/switch region; other site 387092001552 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 387092001553 active site 387092001554 PAS domain; Region: PAS_9; pfam13426 387092001555 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092001556 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092001557 metal binding site [ion binding]; metal-binding site 387092001558 active site 387092001559 I-site; other site 387092001560 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 387092001561 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 387092001562 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 387092001563 acetyl-CoA synthetase; Provisional; Region: PRK00174 387092001564 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 387092001565 active site 387092001566 CoA binding site [chemical binding]; other site 387092001567 acyl-activating enzyme (AAE) consensus motif; other site 387092001568 AMP binding site [chemical binding]; other site 387092001569 acetate binding site [chemical binding]; other site 387092001570 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 387092001571 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 387092001572 active site 387092001573 catalytic site [active] 387092001574 substrate binding site [chemical binding]; other site 387092001575 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 387092001576 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 387092001577 ligand binding site [chemical binding]; other site 387092001578 flexible hinge region; other site 387092001579 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 387092001580 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 387092001581 metal binding triad; other site 387092001582 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 387092001583 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 387092001584 Na binding site [ion binding]; other site 387092001585 Protein of unknown function, DUF485; Region: DUF485; pfam04341 387092001586 outer membrane porin, OprD family; Region: OprD; pfam03573 387092001587 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092001588 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092001589 active site 387092001590 phosphorylation site [posttranslational modification] 387092001591 intermolecular recognition site; other site 387092001592 dimerization interface [polypeptide binding]; other site 387092001593 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 387092001594 DNA binding site [nucleotide binding] 387092001595 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 387092001596 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092001597 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 387092001598 dimer interface [polypeptide binding]; other site 387092001599 phosphorylation site [posttranslational modification] 387092001600 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 387092001601 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 387092001602 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 387092001603 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 387092001604 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 387092001605 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 387092001606 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 387092001607 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 387092001608 active site 387092001609 Zn binding site [ion binding]; other site 387092001610 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 387092001611 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 387092001612 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 387092001613 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 387092001614 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 387092001615 acyl-activating enzyme (AAE) consensus motif; other site 387092001616 putative AMP binding site [chemical binding]; other site 387092001617 putative active site [active] 387092001618 putative CoA binding site [chemical binding]; other site 387092001619 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 387092001620 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 387092001621 active site 387092001622 NAD synthetase; Reviewed; Region: nadE; PRK02628 387092001623 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 387092001624 multimer interface [polypeptide binding]; other site 387092001625 active site 387092001626 catalytic triad [active] 387092001627 protein interface 1 [polypeptide binding]; other site 387092001628 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 387092001629 homodimer interface [polypeptide binding]; other site 387092001630 NAD binding pocket [chemical binding]; other site 387092001631 ATP binding pocket [chemical binding]; other site 387092001632 Mg binding site [ion binding]; other site 387092001633 active-site loop [active] 387092001634 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group; Region: Alpha_ANH_like; cd01986 387092001635 Ligand Binding Site [chemical binding]; other site 387092001636 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 387092001637 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 387092001638 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 387092001639 active site 387092001640 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 387092001641 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 387092001642 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 387092001643 Walker A motif; other site 387092001644 ATP binding site [chemical binding]; other site 387092001645 Walker B motif; other site 387092001646 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 387092001647 rod shape-determining protein MreB; Provisional; Region: PRK13927 387092001648 MreB and similar proteins; Region: MreB_like; cd10225 387092001649 nucleotide binding site [chemical binding]; other site 387092001650 Mg binding site [ion binding]; other site 387092001651 putative protofilament interaction site [polypeptide binding]; other site 387092001652 RodZ interaction site [polypeptide binding]; other site 387092001653 rod shape-determining protein MreC; Provisional; Region: PRK13922 387092001654 rod shape-determining protein MreC; Region: MreC; pfam04085 387092001655 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 387092001656 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 387092001657 ATP-grasp domain; Region: ATP-grasp_4; cl17255 387092001658 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 387092001659 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 387092001660 ATP-grasp domain; Region: ATP-grasp_4; cl17255 387092001661 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 387092001662 IMP binding site; other site 387092001663 dimer interface [polypeptide binding]; other site 387092001664 interdomain contacts; other site 387092001665 partial ornithine binding site; other site 387092001666 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 387092001667 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 387092001668 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092001669 PAS domain; Region: PAS_9; pfam13426 387092001670 putative active site [active] 387092001671 heme pocket [chemical binding]; other site 387092001672 5-methyltetrahydrofolate--homocysteine methyltransferase; Region: metH; TIGR02082 387092001673 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 387092001674 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 387092001675 substrate binding pocket [chemical binding]; other site 387092001676 dimer interface [polypeptide binding]; other site 387092001677 inhibitor binding site; inhibition site 387092001678 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 387092001679 B12 binding site [chemical binding]; other site 387092001680 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 387092001681 Cache domain; Region: Cache_1; pfam02743 387092001682 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092001683 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092001684 metal binding site [ion binding]; metal-binding site 387092001685 active site 387092001686 I-site; other site 387092001687 Domain of Unknown Function (DUF1080); Region: DUF1080; pfam06439 387092001688 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; Region: CobA_CobO_BtuR; pfam02572 387092001689 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 387092001690 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 387092001691 N-terminal plug; other site 387092001692 ligand-binding site [chemical binding]; other site 387092001693 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 387092001694 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 387092001695 active site 387092001696 tetramer interface; other site 387092001697 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 387092001698 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 387092001699 metal binding site [ion binding]; metal-binding site 387092001700 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 387092001701 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 387092001702 minor groove reading motif; other site 387092001703 helix-hairpin-helix signature motif; other site 387092001704 substrate binding pocket [chemical binding]; other site 387092001705 active site 387092001706 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 387092001707 hypothetical protein; Validated; Region: PRK00110 387092001708 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 387092001709 galactinol-raffinose galactosyltransferase/ghydrolase, hydrolyzing O-glycosyl compounds; Region: PLN02982 387092001710 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 387092001711 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 387092001712 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 387092001713 active site 387092001714 intersubunit interface [polypeptide binding]; other site 387092001715 zinc binding site [ion binding]; other site 387092001716 Na+ binding site [ion binding]; other site 387092001717 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 387092001718 active site 387092001719 Zn binding site [ion binding]; other site 387092001720 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 387092001721 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 387092001722 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 387092001723 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 387092001724 catalytic residue [active] 387092001725 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 387092001726 histidinol dehydrogenase; Region: hisD; TIGR00069 387092001727 NAD binding site [chemical binding]; other site 387092001728 dimerization interface [polypeptide binding]; other site 387092001729 product binding site; other site 387092001730 substrate binding site [chemical binding]; other site 387092001731 zinc binding site [ion binding]; other site 387092001732 catalytic residues [active] 387092001733 CHASE4 domain; Region: CHASE4; pfam05228 387092001734 PAS domain S-box; Region: sensory_box; TIGR00229 387092001735 PAS fold; Region: PAS_3; pfam08447 387092001736 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092001737 putative active site [active] 387092001738 heme pocket [chemical binding]; other site 387092001739 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092001740 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092001741 metal binding site [ion binding]; metal-binding site 387092001742 active site 387092001743 I-site; other site 387092001744 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 387092001745 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 387092001746 Phosphate transporter family; Region: PHO4; pfam01384 387092001747 Transcriptional activator; Region: Transcrip_act; pfam04949 387092001748 Phosphate transporter family; Region: PHO4; cl00396 387092001749 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 387092001750 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 387092001751 Initiation factor 2 subunit family; Region: IF-2B; pfam01008 387092001752 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 387092001753 4Fe-4S binding domain; Region: Fer4_6; pfam12837 387092001754 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 387092001755 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 387092001756 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 387092001757 molybdopterin cofactor binding site; other site 387092001758 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 387092001759 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 387092001760 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 387092001761 active site 387092001762 NTP binding site [chemical binding]; other site 387092001763 metal binding triad [ion binding]; metal-binding site 387092001764 antibiotic binding site [chemical binding]; other site 387092001765 Protein of unknown function DUF86; Region: DUF86; cl01031 387092001766 Cytochrome c; Region: Cytochrom_C; cl11414 387092001767 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 387092001768 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 387092001769 4Fe-4S binding domain; Region: Fer4; pfam00037 387092001770 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 387092001771 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 387092001772 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 387092001773 PhoU domain; Region: PhoU; pfam01895 387092001774 PhoU domain; Region: PhoU; pfam01895 387092001775 PBP superfamily domain; Region: PBP_like_2; cl17296 387092001776 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 387092001777 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 387092001778 dimer interface [polypeptide binding]; other site 387092001779 conserved gate region; other site 387092001780 ABC-ATPase subunit interface; other site 387092001781 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 387092001782 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 387092001783 dimer interface [polypeptide binding]; other site 387092001784 conserved gate region; other site 387092001785 ABC-ATPase subunit interface; other site 387092001786 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 387092001787 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 387092001788 Walker A/P-loop; other site 387092001789 ATP binding site [chemical binding]; other site 387092001790 Q-loop/lid; other site 387092001791 ABC transporter signature motif; other site 387092001792 Walker B; other site 387092001793 D-loop; other site 387092001794 H-loop/switch region; other site 387092001795 Protein of unknown function DUF58; Region: DUF58; pfam01882 387092001796 MoxR-like ATPases [General function prediction only]; Region: COG0714 387092001797 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 387092001798 Walker A motif; other site 387092001799 ATP binding site [chemical binding]; other site 387092001800 Walker B motif; other site 387092001801 arginine finger; other site 387092001802 Oxygen tolerance; Region: BatD; pfam13584 387092001803 von Willebrand factor type A domain; Region: VWA_2; pfam13519 387092001804 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 387092001805 binding surface 387092001806 TPR motif; other site 387092001807 Tetratricopeptide repeat; Region: TPR_16; pfam13432 387092001808 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 387092001809 metal ion-dependent adhesion site (MIDAS); other site 387092001810 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 387092001811 tetramer interfaces [polypeptide binding]; other site 387092001812 binuclear metal-binding site [ion binding]; other site 387092001813 ATP sulfurylase (sulfate adenylyltransferase) [Inorganic ion transport and metabolism]; Region: MET3; COG2046 387092001814 PUA-like domain; Region: PUA_2; pfam14306 387092001815 ATP-sulfurylase; Region: ATP-sulfurylase; pfam01747 387092001816 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 387092001817 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092001818 active site 387092001819 phosphorylation site [posttranslational modification] 387092001820 intermolecular recognition site; other site 387092001821 dimerization interface [polypeptide binding]; other site 387092001822 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 387092001823 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 387092001824 substrate binding site; other site 387092001825 dimer interface; other site 387092001826 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 387092001827 homotrimer interaction site [polypeptide binding]; other site 387092001828 zinc binding site [ion binding]; other site 387092001829 CDP-binding sites; other site 387092001830 thiamine biosynthesis protein ThiC; Region: thiC; TIGR00190 387092001831 ThiC family; Region: ThiC; pfam01964 387092001832 Domain of unknown function DUF59; Region: DUF59; pfam01883 387092001833 antiporter inner membrane protein; Provisional; Region: PRK11670 387092001834 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 387092001835 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 387092001836 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 387092001837 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092001838 PAS domain; Region: PAS_9; pfam13426 387092001839 putative active site [active] 387092001840 heme pocket [chemical binding]; other site 387092001841 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 387092001842 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092001843 putative CheW interface [polypeptide binding]; other site 387092001844 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092001845 dimer interface [polypeptide binding]; other site 387092001846 putative CheW interface [polypeptide binding]; other site 387092001847 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 387092001848 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 387092001849 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092001850 active site 387092001851 phosphorylation site [posttranslational modification] 387092001852 intermolecular recognition site; other site 387092001853 dimerization interface [polypeptide binding]; other site 387092001854 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 387092001855 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 387092001856 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092001857 active site 387092001858 phosphorylation site [posttranslational modification] 387092001859 intermolecular recognition site; other site 387092001860 dimerization interface [polypeptide binding]; other site 387092001861 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 387092001862 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 387092001863 putative binding surface; other site 387092001864 active site 387092001865 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 387092001866 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 387092001867 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092001868 ATP binding site [chemical binding]; other site 387092001869 Mg2+ binding site [ion binding]; other site 387092001870 G-X-G motif; other site 387092001871 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 387092001872 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 387092001873 FliG C-terminal domain; Region: FliG_C; pfam01706 387092001874 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 387092001875 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 387092001876 flagellar motor switch protein FliN; Region: fliN; TIGR02480 387092001877 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 387092001878 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 387092001879 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 387092001880 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 387092001881 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 387092001882 SAF-like; Region: SAF_2; pfam13144 387092001883 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 387092001884 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 387092001885 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 387092001886 Flagellar L-ring protein; Region: FlgH; pfam02107 387092001887 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 387092001888 Flagellar P-ring protein; Region: FlgI; pfam02119 387092001889 Rod binding protein; Region: Rod-binding; cl01626 387092001890 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 387092001891 FHIPEP family; Region: FHIPEP; pfam00771 387092001892 Flagellar GTP-binding protein [Cell motility and secretion]; Region: FlhF; COG1419 387092001893 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 387092001894 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 387092001895 Walker A motif; other site 387092001896 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 387092001897 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 387092001898 P-loop; other site 387092001899 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 387092001900 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 387092001901 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 387092001902 DNA binding residues [nucleotide binding] 387092001903 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 387092001904 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 387092001905 TPR motif; other site 387092001906 binding surface 387092001907 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 387092001908 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 387092001909 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 387092001910 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 387092001911 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 387092001912 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 387092001913 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 387092001914 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 387092001915 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 387092001916 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 387092001917 Walker A motif; other site 387092001918 ATP binding site [chemical binding]; other site 387092001919 Walker B motif; other site 387092001920 Flagellar hook capping protein [Cell motility and secretion]; Region: FlgD; COG1843 387092001921 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 387092001922 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 387092001923 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 387092001924 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 387092001925 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 387092001926 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 387092001927 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 387092001928 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 387092001929 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 387092001930 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 387092001931 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 387092001932 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 387092001933 L-lactate permease; Region: Lactate_perm; cl00701 387092001934 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 387092001935 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092001936 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092001937 metal binding site [ion binding]; metal-binding site 387092001938 active site 387092001939 I-site; other site 387092001940 Uncharacterized conserved protein [Function unknown]; Region: COG3334 387092001941 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 387092001942 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 387092001943 PilZ domain; Region: PilZ; pfam07238 387092001944 flagellin; Provisional; Region: PRK12806 387092001945 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 387092001946 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 387092001947 FlaG protein; Region: FlaG; pfam03646 387092001948 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 387092001949 flagellar capping protein; Reviewed; Region: fliD; PRK08032 387092001950 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 387092001951 Flagellar protein FliS; Region: FliS; cl00654 387092001952 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 387092001953 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 387092001954 Flagellar hook-associated protein [Cell motility and secretion]; Region: FlgK; COG1256 387092001955 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 387092001956 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 387092001957 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 387092001958 glutaminase active site [active] 387092001959 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 387092001960 dimer interface [polypeptide binding]; other site 387092001961 active site 387092001962 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 387092001963 dimer interface [polypeptide binding]; other site 387092001964 active site 387092001965 hypothetical protein; Provisional; Region: PRK08444 387092001966 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 387092001967 FeS/SAM binding site; other site 387092001968 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 387092001969 active site 387092001970 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 387092001971 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 387092001972 glutamine binding [chemical binding]; other site 387092001973 catalytic triad [active] 387092001974 ATP citrate (pro-S)-lyase; Region: PLN02235 387092001975 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 387092001976 ATP citrate (pro-S)-lyase; Region: PLN02522 387092001977 CoA-ligase; Region: Ligase_CoA; pfam00549 387092001978 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 387092001979 active site 387092001980 oxalacetate binding site [chemical binding]; other site 387092001981 citrylCoA binding site [chemical binding]; other site 387092001982 coenzyme A binding site [chemical binding]; other site 387092001983 catalytic triad [active] 387092001984 Helix-turn-helix domain; Region: HTH_28; pfam13518 387092001985 putative transposase OrfB; Reviewed; Region: PHA02517 387092001986 Homeodomain-like domain; Region: HTH_32; pfam13565 387092001987 Integrase core domain; Region: rve; pfam00665 387092001988 Integrase core domain; Region: rve_3; pfam13683 387092001989 argininosuccinate lyase; Provisional; Region: PRK00855 387092001990 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 387092001991 active sites [active] 387092001992 tetramer interface [polypeptide binding]; other site 387092001993 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 387092001994 nucleotide binding site/active site [active] 387092001995 HIT family signature motif; other site 387092001996 catalytic residue [active] 387092001997 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 387092001998 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 387092001999 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 387092002000 dimer interface [polypeptide binding]; other site 387092002001 motif 1; other site 387092002002 active site 387092002003 motif 2; other site 387092002004 motif 3; other site 387092002005 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 387092002006 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 387092002007 putative tRNA-binding site [nucleotide binding]; other site 387092002008 tRNA synthetase B5 domain; Region: B5; smart00874 387092002009 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 387092002010 dimer interface [polypeptide binding]; other site 387092002011 motif 1; other site 387092002012 motif 3; other site 387092002013 motif 2; other site 387092002014 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 387092002015 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 387092002016 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 387092002017 hinge; other site 387092002018 active site 387092002019 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 387092002020 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 387092002021 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 387092002022 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 387092002023 RNA binding site [nucleotide binding]; other site 387092002024 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 387092002025 RNA binding site [nucleotide binding]; other site 387092002026 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 387092002027 RNA binding site [nucleotide binding]; other site 387092002028 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 387092002029 RNA binding site [nucleotide binding]; other site 387092002030 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 387092002031 RNA binding site [nucleotide binding]; other site 387092002032 S1 RNA binding domain; Region: S1; pfam00575 387092002033 RNA binding site [nucleotide binding]; other site 387092002034 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 387092002035 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 387092002036 ligand binding site [chemical binding]; other site 387092002037 NAD binding site [chemical binding]; other site 387092002038 dimerization interface [polypeptide binding]; other site 387092002039 catalytic site [active] 387092002040 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 387092002041 putative L-serine binding site [chemical binding]; other site 387092002042 Outer membrane efflux protein; Region: OEP; pfam02321 387092002043 Outer membrane efflux protein; Region: OEP; pfam02321 387092002044 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 387092002045 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092002046 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 387092002047 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 387092002048 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 387092002049 elongation factor P; Validated; Region: PRK00529 387092002050 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 387092002051 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 387092002052 RNA binding site [nucleotide binding]; other site 387092002053 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 387092002054 RNA binding site [nucleotide binding]; other site 387092002055 Cupin domain; Region: Cupin_2; pfam07883 387092002056 DJ-1 family protein; Region: not_thiJ; TIGR01383 387092002057 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 387092002058 conserved cys residue [active] 387092002059 Phospholipid methyltransferase; Region: PEMT; cl17370 387092002060 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 387092002061 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 387092002062 active site 387092002063 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 387092002064 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 387092002065 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 387092002066 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 387092002067 S-adenosylmethionine binding site [chemical binding]; other site 387092002068 shikimate kinase; Reviewed; Region: aroK; PRK00131 387092002069 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 387092002070 ADP binding site [chemical binding]; other site 387092002071 magnesium binding site [ion binding]; other site 387092002072 putative shikimate binding site; other site 387092002073 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 387092002074 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 387092002075 active site 387092002076 PHP Thumb interface [polypeptide binding]; other site 387092002077 metal binding site [ion binding]; metal-binding site 387092002078 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 387092002079 generic binding surface II; other site 387092002080 generic binding surface I; other site 387092002081 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 387092002082 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 387092002083 Peptidase family M54, also called archaemetzincins or archaelysins; Region: Peptidase_M54; cd11375 387092002084 active site 387092002085 Zn binding site [ion binding]; other site 387092002086 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 387092002087 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 387092002088 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 387092002089 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092002090 PAS domain; Region: PAS_9; pfam13426 387092002091 putative active site [active] 387092002092 heme pocket [chemical binding]; other site 387092002093 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 387092002094 GAF domain; Region: GAF; pfam01590 387092002095 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092002096 PAS domain; Region: PAS_9; pfam13426 387092002097 putative active site [active] 387092002098 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092002099 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092002100 metal binding site [ion binding]; metal-binding site 387092002101 active site 387092002102 I-site; other site 387092002103 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 387092002104 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 387092002105 active site 387092002106 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 387092002107 Fe-S cluster binding site [ion binding]; other site 387092002108 active site 387092002109 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 387092002110 Cysteine-rich domain; Region: CCG; pfam02754 387092002111 Cysteine-rich domain; Region: CCG; pfam02754 387092002112 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 387092002113 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 387092002114 catalytic loop [active] 387092002115 iron binding site [ion binding]; other site 387092002116 L-aspartate oxidase; Provisional; Region: PRK06175 387092002117 succinate dehydrogenase or fumarate reductase, flavoprotein subunitGram-negative/mitochondrial subgroup; Region: sdhA_frdA_Gneg; TIGR01812 387092002118 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 387092002119 thiamine monophosphate kinase; Provisional; Region: PRK05731 387092002120 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 387092002121 ATP binding site [chemical binding]; other site 387092002122 dimerization interface [polypeptide binding]; other site 387092002123 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 387092002124 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 387092002125 Permutation of conserved domain; other site 387092002126 active site 387092002127 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092002128 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092002129 metal binding site [ion binding]; metal-binding site 387092002130 active site 387092002131 I-site; other site 387092002132 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 387092002133 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 387092002134 catalytic residue [active] 387092002135 RIP metalloprotease RseP; Region: TIGR00054 387092002136 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 387092002137 active site 387092002138 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 387092002139 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 387092002140 putative substrate binding region [chemical binding]; other site 387092002141 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 387092002142 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 387092002143 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 387092002144 putative NAD(P) binding site [chemical binding]; other site 387092002145 active site 387092002146 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 387092002147 dihydrodipicolinate synthase; Region: dapA; TIGR00674 387092002148 dimer interface [polypeptide binding]; other site 387092002149 active site 387092002150 catalytic residue [active] 387092002151 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 387092002152 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 387092002153 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 387092002154 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 387092002155 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 387092002156 quinone interaction residues [chemical binding]; other site 387092002157 active site 387092002158 catalytic residues [active] 387092002159 FMN binding site [chemical binding]; other site 387092002160 substrate binding site [chemical binding]; other site 387092002161 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 387092002162 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 387092002163 S-adenosylmethionine binding site [chemical binding]; other site 387092002164 GTP-binding protein YchF; Reviewed; Region: PRK09601 387092002165 YchF GTPase; Region: YchF; cd01900 387092002166 G1 box; other site 387092002167 GTP/Mg2+ binding site [chemical binding]; other site 387092002168 Switch I region; other site 387092002169 G2 box; other site 387092002170 Switch II region; other site 387092002171 G3 box; other site 387092002172 G4 box; other site 387092002173 G5 box; other site 387092002174 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 387092002175 multifunctional aminopeptidase A; Provisional; Region: PRK00913 387092002176 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 387092002177 interface (dimer of trimers) [polypeptide binding]; other site 387092002178 Substrate-binding/catalytic site; other site 387092002179 Zn-binding sites [ion binding]; other site 387092002180 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 387092002181 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 387092002182 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 387092002183 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 387092002184 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092002185 catalytic residue [active] 387092002186 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 387092002187 active site 387092002188 ribose-5-phosphate isomerase B; Provisional; Region: PRK05571 387092002189 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 387092002190 Peptidase family M50; Region: Peptidase_M50; pfam02163 387092002191 active site 387092002192 putative substrate binding region [chemical binding]; other site 387092002193 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 387092002194 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 387092002195 Catalytic site [active] 387092002196 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 387092002197 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14183 387092002198 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 387092002199 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 387092002200 homodimer interface [polypeptide binding]; other site 387092002201 NADP binding site [chemical binding]; other site 387092002202 substrate binding site [chemical binding]; other site 387092002203 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 387092002204 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]; Region: COG3260 387092002205 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 387092002206 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 387092002207 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 387092002208 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 387092002209 Hydrogenase 4 membrane component (E) [Energy production and conversion]; Region: HyfE; cl17899 387092002210 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 387092002211 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 387092002212 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 387092002213 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 387092002214 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 387092002215 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 387092002216 inhibitor-cofactor binding pocket; inhibition site 387092002217 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092002218 catalytic residue [active] 387092002219 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 387092002220 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 387092002221 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 387092002222 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 387092002223 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 387092002224 DNA binding residues [nucleotide binding] 387092002225 Helix-turn-helix domain; Region: HTH_28; pfam13518 387092002226 putative transposase OrfB; Reviewed; Region: PHA02517 387092002227 Homeodomain-like domain; Region: HTH_32; pfam13565 387092002228 Integrase core domain; Region: rve; pfam00665 387092002229 Integrase core domain; Region: rve_3; pfam13683 387092002230 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 387092002231 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 387092002232 substrate binding site [chemical binding]; other site 387092002233 tartrate dehydrogenase; Region: TTC; TIGR02089 387092002234 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 387092002235 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 387092002236 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 387092002237 active site 387092002238 NTP binding site [chemical binding]; other site 387092002239 metal binding triad [ion binding]; metal-binding site 387092002240 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 387092002241 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 387092002242 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 387092002243 putative active site [active] 387092002244 putative substrate binding site [chemical binding]; other site 387092002245 putative cosubstrate binding site; other site 387092002246 catalytic site [active] 387092002247 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 387092002248 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 387092002249 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 387092002250 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 387092002251 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 387092002252 ferrochelatase; Reviewed; Region: hemH; PRK00035 387092002253 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 387092002254 C-terminal domain interface [polypeptide binding]; other site 387092002255 active site 387092002256 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 387092002257 active site 387092002258 N-terminal domain interface [polypeptide binding]; other site 387092002259 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 387092002260 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII; cd09992 387092002261 active site 387092002262 Zn binding site [ion binding]; other site 387092002263 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 387092002264 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 387092002265 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092002266 Walker A/P-loop; other site 387092002267 ATP binding site [chemical binding]; other site 387092002268 Q-loop/lid; other site 387092002269 ABC transporter signature motif; other site 387092002270 Walker B; other site 387092002271 D-loop; other site 387092002272 H-loop/switch region; other site 387092002273 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 387092002274 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 387092002275 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 387092002276 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 387092002277 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 387092002278 Peptidase M15; Region: Peptidase_M15_3; cl01194 387092002279 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 387092002280 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 387092002281 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 387092002282 Probable gene remnant. Similar to the N-terminal region of Symbiobacterium thermophilum IAM 14863 ATP-dependent helicase (898 aa) STH2293. This CDS is disrupted by the insertion of IS element following codon 668, and contains a frameshift mutation following codon 299. 387092002283 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 387092002284 Transposase; Region: HTH_Tnp_1; cl17663 387092002285 IS2 transposase TnpB; Reviewed; Region: PRK09409 387092002286 HTH-like domain; Region: HTH_21; pfam13276 387092002287 Integrase core domain; Region: rve; pfam00665 387092002288 Integrase core domain; Region: rve_3; pfam13683 387092002289 Protein of unknown function (DUF4065); Region: DUF4065; pfam13274 387092002290 Probable gene remnant. Similar to the C-terminal region of Carboxydothermus hydrogenoformans Z-2901 type II restriction enzyme, methylase subunit (1207 aa) CHY_2653. 387092002291 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 387092002292 TIGR02687 family protein; Region: TIGR02687 387092002293 PglZ domain; Region: PglZ; pfam08665 387092002294 conserved hypothetical protein; Region: Lon_rel_chp; TIGR02653 387092002295 Putative ATP-dependent Lon protease; Region: Lon_2; pfam13337 387092002296 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 387092002297 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 387092002298 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 387092002299 RNA binding surface [nucleotide binding]; other site 387092002300 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 387092002301 active site 387092002302 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 387092002303 Interdomain contacts; other site 387092002304 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 387092002305 Cytokine receptor motif; other site 387092002306 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 387092002307 Interdomain contacts; other site 387092002308 Cytokine receptor motif; other site 387092002309 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 387092002310 Interdomain contacts; other site 387092002311 Cytokine receptor motif; other site 387092002312 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 387092002313 S-adenosylmethionine binding site [chemical binding]; other site 387092002314 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 387092002315 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 387092002316 Walker A/P-loop; other site 387092002317 ATP binding site [chemical binding]; other site 387092002318 Q-loop/lid; other site 387092002319 ABC transporter signature motif; other site 387092002320 Walker B; other site 387092002321 D-loop; other site 387092002322 H-loop/switch region; other site 387092002323 Peptidase family M23; Region: Peptidase_M23; pfam01551 387092002324 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 387092002325 putative nucleotide binding site [chemical binding]; other site 387092002326 uridine monophosphate binding site [chemical binding]; other site 387092002327 homohexameric interface [polypeptide binding]; other site 387092002328 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 387092002329 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 387092002330 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 387092002331 Zn2+ binding site [ion binding]; other site 387092002332 Mg2+ binding site [ion binding]; other site 387092002333 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 387092002334 synthetase active site [active] 387092002335 NTP binding site [chemical binding]; other site 387092002336 metal binding site [ion binding]; metal-binding site 387092002337 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 387092002338 ACT domain; Region: ACT; pfam01842 387092002339 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 387092002340 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 387092002341 active site 387092002342 HIGH motif; other site 387092002343 dimer interface [polypeptide binding]; other site 387092002344 KMSKS motif; other site 387092002345 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 387092002346 RNA binding surface [nucleotide binding]; other site 387092002347 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 387092002348 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 387092002349 FMN binding site [chemical binding]; other site 387092002350 substrate binding site [chemical binding]; other site 387092002351 putative catalytic residue [active] 387092002352 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 387092002353 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 387092002354 active site 387092002355 metal binding site [ion binding]; metal-binding site 387092002356 Transcriptional regulator; Region: Rrf2; pfam02082 387092002357 Rrf2 family protein; Region: rrf2_super; TIGR00738 387092002358 Domain of unknown function (DUF4395); Region: DUF4395; pfam14340 387092002359 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 387092002360 dimer interface [polypeptide binding]; other site 387092002361 substrate binding site [chemical binding]; other site 387092002362 metal binding sites [ion binding]; metal-binding site 387092002363 Protein of unknown function (DUF503); Region: DUF503; cl00669 387092002364 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 387092002365 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 387092002366 putative MPT binding site; other site 387092002367 adenylate kinase; Reviewed; Region: adk; PRK00279 387092002368 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 387092002369 AMP-binding site [chemical binding]; other site 387092002370 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 387092002371 FeoA domain; Region: FeoA; pfam04023 387092002372 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 387092002373 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 387092002374 dimer interface [polypeptide binding]; other site 387092002375 anticodon binding site; other site 387092002376 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 387092002377 homodimer interface [polypeptide binding]; other site 387092002378 motif 1; other site 387092002379 active site 387092002380 motif 2; other site 387092002381 GAD domain; Region: GAD; pfam02938 387092002382 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 387092002383 active site 387092002384 motif 3; other site 387092002385 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 387092002386 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 387092002387 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 387092002388 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092002389 Walker A/P-loop; other site 387092002390 ATP binding site [chemical binding]; other site 387092002391 Q-loop/lid; other site 387092002392 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 387092002393 ABC transporter signature motif; other site 387092002394 Walker B; other site 387092002395 D-loop; other site 387092002396 H-loop/switch region; other site 387092002397 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 387092002398 active site 387092002399 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 387092002400 N-acetyl-D-glucosamine binding site [chemical binding]; other site 387092002401 catalytic residue [active] 387092002402 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 387092002403 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 387092002404 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 387092002405 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 387092002406 Sporulation related domain; Region: SPOR; pfam05036 387092002407 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 387092002408 putative active site pocket [active] 387092002409 4-fold oligomerization interface [polypeptide binding]; other site 387092002410 metal binding residues [ion binding]; metal-binding site 387092002411 3-fold/trimer interface [polypeptide binding]; other site 387092002412 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 387092002413 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 387092002414 active site 387092002415 motif I; other site 387092002416 motif II; other site 387092002417 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 387092002418 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 387092002419 OstA-like protein; Region: OstA; pfam03968 387092002420 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 387092002421 G1 box; other site 387092002422 GTP/Mg2+ binding site [chemical binding]; other site 387092002423 Switch I region; other site 387092002424 G2 box; other site 387092002425 G3 box; other site 387092002426 Switch II region; other site 387092002427 G4 box; other site 387092002428 G5 box; other site 387092002429 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 387092002430 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 387092002431 Coenzyme A binding pocket [chemical binding]; other site 387092002432 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 387092002433 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 387092002434 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 387092002435 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 387092002436 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 387092002437 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 387092002438 metal-binding heat shock protein; Provisional; Region: PRK00016 387092002439 Nitrate and nitrite sensing; Region: NIT; pfam08376 387092002440 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 387092002441 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 387092002442 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092002443 dimer interface [polypeptide binding]; other site 387092002444 putative CheW interface [polypeptide binding]; other site 387092002445 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 387092002446 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 387092002447 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 387092002448 Ligand Binding Site [chemical binding]; other site 387092002449 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 387092002450 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 387092002451 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 387092002452 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 387092002453 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 387092002454 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 387092002455 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 387092002456 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 387092002457 active site 387092002458 HIGH motif; other site 387092002459 KMSKS motif; other site 387092002460 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 387092002461 anticodon binding site; other site 387092002462 tRNA binding surface [nucleotide binding]; other site 387092002463 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 387092002464 dimer interface [polypeptide binding]; other site 387092002465 putative tRNA-binding site [nucleotide binding]; other site 387092002466 fructose-1,6-bisphosphatase; Provisional; Region: PRK09293 387092002467 active site 387092002468 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 387092002469 Walker A motif; other site 387092002470 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 387092002471 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 387092002472 N-acetyl-D-glucosamine binding site [chemical binding]; other site 387092002473 catalytic residue [active] 387092002474 YGGT family; Region: YGGT; pfam02325 387092002475 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 387092002476 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387092002477 active site 387092002478 HIGH motif; other site 387092002479 nucleotide binding site [chemical binding]; other site 387092002480 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 387092002481 active site 387092002482 KMSKS motif; other site 387092002483 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 387092002484 outer membrane porin, OprD family; Region: OprD; pfam03573 387092002485 FeoA domain; Region: FeoA; pfam04023 387092002486 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 387092002487 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 387092002488 G1 box; other site 387092002489 GTP/Mg2+ binding site [chemical binding]; other site 387092002490 Switch I region; other site 387092002491 G2 box; other site 387092002492 G3 box; other site 387092002493 Switch II region; other site 387092002494 G4 box; other site 387092002495 G5 box; other site 387092002496 Nucleoside recognition; Region: Gate; pfam07670 387092002497 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 387092002498 Nucleoside recognition; Region: Gate; pfam07670 387092002499 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 387092002500 threonine dehydratase; Provisional; Region: PRK08526 387092002501 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 387092002502 tetramer interface [polypeptide binding]; other site 387092002503 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092002504 catalytic residue [active] 387092002505 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 387092002506 exopolyphosphatase; Region: exo_poly_only; TIGR03706 387092002507 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 387092002508 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK08527 387092002509 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 387092002510 PYR/PP interface [polypeptide binding]; other site 387092002511 dimer interface [polypeptide binding]; other site 387092002512 TPP binding site [chemical binding]; other site 387092002513 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 387092002514 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 387092002515 TPP-binding site [chemical binding]; other site 387092002516 dimer interface [polypeptide binding]; other site 387092002517 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 387092002518 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 387092002519 putative valine binding site [chemical binding]; other site 387092002520 dimer interface [polypeptide binding]; other site 387092002521 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 387092002522 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 387092002523 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 387092002524 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 387092002525 trimer interface [polypeptide binding]; other site 387092002526 active site 387092002527 UDP-GlcNAc binding site [chemical binding]; other site 387092002528 lipid binding site [chemical binding]; lipid-binding site 387092002529 ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent; Region: RTPR; TIGR02505 387092002530 Class II ribonucleotide reductase, monomeric form; Region: RNR_II_monomer; cd01676 387092002531 putative active site [active] 387092002532 aspartate aminotransferase; Provisional; Region: PRK05764 387092002533 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 387092002534 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092002535 homodimer interface [polypeptide binding]; other site 387092002536 catalytic residue [active] 387092002537 serine O-acetyltransferase; Region: cysE; TIGR01172 387092002538 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 387092002539 trimer interface [polypeptide binding]; other site 387092002540 active site 387092002541 substrate binding site [chemical binding]; other site 387092002542 CoA binding site [chemical binding]; other site 387092002543 arginine decarboxylase; Provisional; Region: PRK05354 387092002544 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 387092002545 dimer interface [polypeptide binding]; other site 387092002546 active site 387092002547 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 387092002548 catalytic residues [active] 387092002549 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 387092002550 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 387092002551 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 387092002552 dimer interface [polypeptide binding]; other site 387092002553 motif 1; other site 387092002554 active site 387092002555 motif 2; other site 387092002556 motif 3; other site 387092002557 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 387092002558 anticodon binding site; other site 387092002559 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 387092002560 thymidylate kinase; Validated; Region: tmk; PRK00698 387092002561 TMP-binding site; other site 387092002562 ATP-binding site [chemical binding]; other site 387092002563 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 387092002564 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 387092002565 active site 387092002566 (T/H)XGH motif; other site 387092002567 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 387092002568 Flavoprotein; Region: Flavoprotein; pfam02441 387092002569 septum formation inhibitor; Reviewed; Region: minC; PRK00556 387092002570 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 387092002571 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 387092002572 Switch I; other site 387092002573 Switch II; other site 387092002574 Septum formation topological specificity factor MinE; Region: MinE; cl00538 387092002575 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 387092002576 IHF dimer interface [polypeptide binding]; other site 387092002577 IHF - DNA interface [nucleotide binding]; other site 387092002578 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 387092002579 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 387092002580 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 387092002581 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 387092002582 Uncharacterized conserved protein [Function unknown]; Region: COG2433 387092002583 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 387092002584 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 387092002585 substrate binding site [chemical binding]; other site 387092002586 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 387092002587 substrate binding site [chemical binding]; other site 387092002588 ligand binding site [chemical binding]; other site 387092002589 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 387092002590 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 387092002591 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 387092002592 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 387092002593 nucleotide binding region [chemical binding]; other site 387092002594 ATP-binding site [chemical binding]; other site 387092002595 SEC-C motif; Region: SEC-C; pfam02810 387092002596 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 387092002597 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 387092002598 FtsX-like permease family; Region: FtsX; pfam02687 387092002599 Protein of unknown function; Region: DUF3971; pfam13116 387092002600 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 387092002601 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 387092002602 dimerization interface [polypeptide binding]; other site 387092002603 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 387092002604 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 387092002605 malate dehydrogenase; Reviewed; Region: PRK06223 387092002606 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 387092002607 NAD(P) binding site [chemical binding]; other site 387092002608 dimer interface [polypeptide binding]; other site 387092002609 tetramer (dimer of dimers) interface [polypeptide binding]; other site 387092002610 substrate binding site [chemical binding]; other site 387092002611 fumarate hydratase; Provisional; Region: PRK06246 387092002612 Fumarase C-terminus; Region: Fumerase_C; cl00795 387092002613 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 387092002614 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 387092002615 CoA-ligase; Region: Ligase_CoA; pfam00549 387092002616 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 387092002617 CoA binding domain; Region: CoA_binding; smart00881 387092002618 CoA-ligase; Region: Ligase_CoA; pfam00549 387092002619 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 387092002620 metal-binding site [ion binding] 387092002621 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 387092002622 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 387092002623 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 387092002624 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 387092002625 dimer interface [polypeptide binding]; other site 387092002626 PYR/PP interface [polypeptide binding]; other site 387092002627 TPP binding site [chemical binding]; other site 387092002628 substrate binding site [chemical binding]; other site 387092002629 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 387092002630 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 387092002631 TPP-binding site [chemical binding]; other site 387092002632 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 387092002633 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 387092002634 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 387092002635 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 387092002636 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 387092002637 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 387092002638 DNA binding site [nucleotide binding] 387092002639 active site 387092002640 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 387092002641 RNA binding surface [nucleotide binding]; other site 387092002642 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 387092002643 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 387092002644 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 387092002645 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 387092002646 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 387092002647 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 387092002648 Walker A/P-loop; other site 387092002649 ATP binding site [chemical binding]; other site 387092002650 Q-loop/lid; other site 387092002651 ABC transporter signature motif; other site 387092002652 Walker B; other site 387092002653 D-loop; other site 387092002654 H-loop/switch region; other site 387092002655 Protein of unknown function (DUF2400); Region: DUF2400; pfam09674 387092002656 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 387092002657 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 387092002658 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 387092002659 thiamine phosphate binding site [chemical binding]; other site 387092002660 active site 387092002661 pyrophosphate binding site [ion binding]; other site 387092002662 hypothetical protein; Provisional; Region: PRK04233 387092002663 SEC-C motif; Region: SEC-C; pfam02810 387092002664 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 387092002665 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 387092002666 GatB domain; Region: GatB_Yqey; smart00845 387092002667 Ion channel; Region: Ion_trans_2; pfam07885 387092002668 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 387092002669 TrkA-N domain; Region: TrkA_N; pfam02254 387092002670 TrkA-C domain; Region: TrkA_C; pfam02080 387092002671 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 387092002672 TrkA-N domain; Region: TrkA_N; pfam02254 387092002673 TrkA-C domain; Region: TrkA_C; pfam02080 387092002674 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 387092002675 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 387092002676 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 387092002677 HDOD domain; Region: HDOD; pfam08668 387092002678 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 387092002679 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 387092002680 putative catalytic cysteine [active] 387092002681 CheB methylesterase; Region: CheB_methylest; pfam01339 387092002682 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 387092002683 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 387092002684 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 387092002685 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 387092002686 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 387092002687 PhnA protein; Region: PhnA; pfam03831 387092002688 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 387092002689 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 387092002690 Walker A/P-loop; other site 387092002691 ATP binding site [chemical binding]; other site 387092002692 Q-loop/lid; other site 387092002693 ABC transporter signature motif; other site 387092002694 Walker B; other site 387092002695 D-loop; other site 387092002696 H-loop/switch region; other site 387092002697 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092002698 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092002699 metal binding site [ion binding]; metal-binding site 387092002700 active site 387092002701 I-site; other site 387092002702 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 387092002703 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 387092002704 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 387092002705 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 387092002706 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 387092002707 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 387092002708 putative acyl-acceptor binding pocket; other site 387092002709 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 387092002710 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 387092002711 putative active site [active] 387092002712 catalytic triad [active] 387092002713 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; pfam02700 387092002714 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 387092002715 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 387092002716 ATP binding site [chemical binding]; other site 387092002717 active site 387092002718 substrate binding site [chemical binding]; other site 387092002719 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 387092002720 C-terminal peptidase (prc); Region: prc; TIGR00225 387092002721 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 387092002722 protein binding site [polypeptide binding]; other site 387092002723 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 387092002724 Catalytic dyad [active] 387092002725 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 387092002726 Clp amino terminal domain; Region: Clp_N; pfam02861 387092002727 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 387092002728 Walker A motif; other site 387092002729 ATP binding site [chemical binding]; other site 387092002730 Walker B motif; other site 387092002731 arginine finger; other site 387092002732 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 387092002733 Walker A motif; other site 387092002734 ATP binding site [chemical binding]; other site 387092002735 Walker B motif; other site 387092002736 arginine finger; other site 387092002737 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 387092002738 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092002739 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092002740 metal binding site [ion binding]; metal-binding site 387092002741 active site 387092002742 I-site; other site 387092002743 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 387092002744 Ribonuclease P; Region: Ribonuclease_P; pfam00825 387092002745 Haemolytic domain; Region: Haemolytic; pfam01809 387092002746 membrane protein insertase; Provisional; Region: PRK01318 387092002747 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 387092002748 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 387092002749 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 387092002750 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 387092002751 trmE is a tRNA modification GTPase; Region: trmE; cd04164 387092002752 G1 box; other site 387092002753 GTP/Mg2+ binding site [chemical binding]; other site 387092002754 Switch I region; other site 387092002755 G2 box; other site 387092002756 Switch II region; other site 387092002757 G3 box; other site 387092002758 G4 box; other site 387092002759 G5 box; other site 387092002760 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 387092002761 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 387092002762 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 387092002763 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 387092002764 THF binding site; other site 387092002765 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 387092002766 substrate binding site [chemical binding]; other site 387092002767 THF binding site; other site 387092002768 zinc-binding site [ion binding]; other site 387092002769 Peptidase M14 Aspartoacylase (ASPA) subfamily; Region: M14_ASPA; cd06909 387092002770 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 387092002771 active site 387092002772 Zn binding site [ion binding]; other site 387092002773 heat shock protein HtpX; Provisional; Region: PRK05457 387092002774 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 387092002775 hypothetical protein; Provisional; Region: PRK07338 387092002776 metal binding site [ion binding]; metal-binding site 387092002777 dimer interface [polypeptide binding]; other site 387092002778 ATP-grasp domain; Region: ATP-grasp_4; cl17255 387092002779 ATP-grasp domain; Region: ATP-grasp_4; cl17255 387092002780 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 387092002781 active site 387092002782 Zn binding site [ion binding]; other site 387092002783 Fibronectin type 3 domain; Region: FN3; smart00060 387092002784 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 387092002785 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 387092002786 dimerization interface [polypeptide binding]; other site 387092002787 ATP binding site [chemical binding]; other site 387092002788 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 387092002789 dimerization interface [polypeptide binding]; other site 387092002790 ATP binding site [chemical binding]; other site 387092002791 Domain of unknown function (DUF389); Region: DUF389; pfam04087 387092002792 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 387092002793 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 387092002794 active site 387092002795 ADP/pyrophosphate binding site [chemical binding]; other site 387092002796 dimerization interface [polypeptide binding]; other site 387092002797 allosteric effector site; other site 387092002798 fructose-1,6-bisphosphate binding site; other site 387092002799 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 387092002800 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092002801 ATP binding site [chemical binding]; other site 387092002802 Mg2+ binding site [ion binding]; other site 387092002803 G-X-G motif; other site 387092002804 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092002805 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092002806 active site 387092002807 phosphorylation site [posttranslational modification] 387092002808 intermolecular recognition site; other site 387092002809 dimerization interface [polypeptide binding]; other site 387092002810 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 387092002811 DNA binding site [nucleotide binding] 387092002812 Pseudogene. Similar to copper-translocating P-type ATPase. This CDS appears to have a frameshift mutation following codon 493. 387092002813 Probable gene remnant. Similar to the C-terminal region of Thiomicrospira crunogena XCL-2 copper-translocating P-type ATPase (670 aa) Tcr_0943. 387092002814 Probable gene remnant. Similar to the N-terminal region of Thiomicrospira crunogena XCL-2 copper-translocating P-type ATPase (670 aa) Tcr_0943. 387092002815 Short C-terminal domain; Region: SHOCT; pfam09851 387092002816 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 387092002817 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 387092002818 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 387092002819 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092002820 Outer membrane efflux protein; Region: OEP; pfam02321 387092002821 Outer membrane efflux protein; Region: OEP; pfam02321 387092002822 YtkA-like; Region: YtkA; pfam13115 387092002823 Predicted permeases [General function prediction only]; Region: COG0701 387092002824 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 387092002825 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 387092002826 dimerization interface [polypeptide binding]; other site 387092002827 putative DNA binding site [nucleotide binding]; other site 387092002828 putative Zn2+ binding site [ion binding]; other site 387092002829 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 387092002830 Outer membrane efflux protein; Region: OEP; pfam02321 387092002831 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 387092002832 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 387092002833 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092002834 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 387092002835 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092002836 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092002837 ATP binding site [chemical binding]; other site 387092002838 Mg2+ binding site [ion binding]; other site 387092002839 G-X-G motif; other site 387092002840 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092002841 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092002842 active site 387092002843 phosphorylation site [posttranslational modification] 387092002844 intermolecular recognition site; other site 387092002845 dimerization interface [polypeptide binding]; other site 387092002846 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 387092002847 DNA binding site [nucleotide binding] 387092002848 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 387092002849 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 387092002850 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 387092002851 dimerization interface [polypeptide binding]; other site 387092002852 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092002853 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092002854 metal binding site [ion binding]; metal-binding site 387092002855 active site 387092002856 I-site; other site 387092002857 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 387092002858 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 387092002859 dimerization interface [polypeptide binding]; other site 387092002860 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 387092002861 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092002862 dimer interface [polypeptide binding]; other site 387092002863 putative CheW interface [polypeptide binding]; other site 387092002864 CheB methylesterase; Region: CheB_methylest; pfam01339 387092002865 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 387092002866 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 387092002867 S-adenosylmethionine binding site [chemical binding]; other site 387092002868 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 387092002869 FeS/SAM binding site; other site 387092002870 Radical SAM superfamily; Region: Radical_SAM; pfam04055 387092002871 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 387092002872 catalytic core [active] 387092002873 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 387092002874 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK07729 387092002875 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 387092002876 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 387092002877 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 387092002878 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 387092002879 Beta-Casp domain; Region: Beta-Casp; smart01027 387092002880 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 387092002881 phosphoenolpyruvate synthase; Validated; Region: PRK06464 387092002882 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 387092002883 Phosphohistidine swiveling domain [Signal transduction mechanisms]; Region: COG3848 387092002884 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 387092002885 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 387092002886 CoA binding domain; Region: CoA_binding_2; pfam13380 387092002887 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 387092002888 lipoyl synthase; Provisional; Region: PRK05481 387092002889 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 387092002890 FeS/SAM binding site; other site 387092002891 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 387092002892 aldolase; Validated; Region: PRK06852 387092002893 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism]; Region: FbaB; COG1830 387092002894 catalytic residue [active] 387092002895 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 387092002896 Predicted membrane protein [Function unknown]; Region: COG3174 387092002897 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 387092002898 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 387092002899 plasma-membrane proton-efflux P-type ATPase; Region: ATPase-IIIA_H; TIGR01647 387092002900 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 387092002901 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 387092002902 Soluble P-type ATPase [General function prediction only]; Region: COG4087 387092002903 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 387092002904 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 387092002905 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 387092002906 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 387092002907 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 387092002908 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 387092002909 E3 interaction surface; other site 387092002910 lipoyl attachment site [posttranslational modification]; other site 387092002911 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 387092002912 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 387092002913 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 387092002914 alpha subunit interface [polypeptide binding]; other site 387092002915 TPP binding site [chemical binding]; other site 387092002916 heterodimer interface [polypeptide binding]; other site 387092002917 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 387092002918 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 387092002919 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 387092002920 tetramer interface [polypeptide binding]; other site 387092002921 TPP-binding site [chemical binding]; other site 387092002922 heterodimer interface [polypeptide binding]; other site 387092002923 phosphorylation loop region [posttranslational modification] 387092002924 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 387092002925 glycogen branching enzyme; Provisional; Region: PRK12313 387092002926 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 387092002927 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 387092002928 active site 387092002929 catalytic site [active] 387092002930 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 387092002931 glycogen synthase; Provisional; Region: glgA; PRK00654 387092002932 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 387092002933 ADP-binding pocket [chemical binding]; other site 387092002934 homodimer interface [polypeptide binding]; other site 387092002935 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 387092002936 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 387092002937 nucleotide binding site [chemical binding]; other site 387092002938 ADP-glucose phosphorylase; Region: PLN02643 387092002939 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 387092002940 nucleotide binding site/active site [active] 387092002941 HIT family signature motif; other site 387092002942 catalytic residue [active] 387092002943 N-terminal catalytic domain of 4-alpha-glucanotransferase; glycoside hydrolase family 57 (GH57); Region: GH57N_TLGT_like; cd10793 387092002944 active site 387092002945 catalytic site [active] 387092002946 homodimer interface [polypeptide binding]; other site 387092002947 Lid 1; other site 387092002948 Domain of unknown function (DUF1925); Region: DUF1925; pfam09094 387092002949 Domain of unknown function (DUF1926); Region: DUF1926; pfam09095 387092002950 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 387092002951 N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57); Region: GH57N_APU; cd10796 387092002952 putative active site [active] 387092002953 catalytic site [active] 387092002954 Pseudogene. Similar to mannose-1-phosphate guanylyltransferase. This CDS appears to have a frameshift mutation following codon 257. 387092002955 Probable gene remnant. Similar to the C-terminal region of Aquifex aeolicus VF5 mannose-1-phosphate guanylyltransferase (831 aa) aq_718. 387092002956 Probable gene remnant. Similar to the N-terminal region of Aquifex aeolicus VF5 mannose-1-phosphate guanylyltransferase (831 aa) aq_718. 387092002957 N-terminal Early set domain, a glycogen binding domain, associated with the catalytic domain of AMP-activated protein kinase beta subunit; Region: E_set_AMPKbeta_like_N; cd02859 387092002958 glycogen binding site [chemical binding]; other site 387092002959 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 387092002960 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 387092002961 glucose-6-phosphate isomerase; Provisional; Region: PRK03868 387092002962 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 387092002963 dimer interface [polypeptide binding]; other site 387092002964 active site 387092002965 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 387092002966 dimer interface [polypeptide binding]; other site 387092002967 active site 387092002968 phosphoglucomutase; Validated; Region: PRK07564 387092002969 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 387092002970 active site 387092002971 substrate binding site [chemical binding]; other site 387092002972 metal binding site [ion binding]; metal-binding site 387092002973 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 387092002974 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 387092002975 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 387092002976 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 387092002977 purine monophosphate binding site [chemical binding]; other site 387092002978 dimer interface [polypeptide binding]; other site 387092002979 putative catalytic residues [active] 387092002980 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 387092002981 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 387092002982 Protein of unknown function DUF72; Region: DUF72; pfam01904 387092002983 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 387092002984 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 387092002985 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 387092002986 N-terminal plug; other site 387092002987 ligand-binding site [chemical binding]; other site 387092002988 Nitrite and sulphite reductase 4Fe-4S domain; Region: NIR_SIR; pfam01077 387092002989 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 387092002990 Nitrite and sulphite reductase 4Fe-4S domain; Region: NIR_SIR; pfam01077 387092002991 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 387092002992 G1 box; other site 387092002993 GTP/Mg2+ binding site [chemical binding]; other site 387092002994 G2 box; other site 387092002995 Switch I region; other site 387092002996 G3 box; other site 387092002997 Switch II region; other site 387092002998 G4 box; other site 387092002999 heat shock protein 90; Provisional; Region: PRK05218 387092003000 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092003001 ATP binding site [chemical binding]; other site 387092003002 Mg2+ binding site [ion binding]; other site 387092003003 G-X-G motif; other site 387092003004 chaperone protein DnaJ; Provisional; Region: PRK14299 387092003005 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 387092003006 HSP70 interaction site [polypeptide binding]; other site 387092003007 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 387092003008 substrate binding site [polypeptide binding]; other site 387092003009 dimer interface [polypeptide binding]; other site 387092003010 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 387092003011 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 387092003012 DNA binding residues [nucleotide binding] 387092003013 putative dimer interface [polypeptide binding]; other site 387092003014 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 387092003015 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 387092003016 hinge; other site 387092003017 active site 387092003018 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 387092003019 S-adenosylmethionine binding site [chemical binding]; other site 387092003020 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 387092003021 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 387092003022 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 387092003023 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 387092003024 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 387092003025 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 387092003026 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 387092003027 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 387092003028 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 387092003029 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 387092003030 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 387092003031 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 387092003032 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 387092003033 putative substrate-binding site; other site 387092003034 nickel binding site [ion binding]; other site 387092003035 HypF finger; Region: zf-HYPF; pfam07503 387092003036 Bacteriophage N adsorption protein A C-term; Region: NfrA_C; pfam13283 387092003037 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 387092003038 Acylphosphatase; Region: Acylphosphatase; pfam00708 387092003039 HypF finger; Region: zf-HYPF; pfam07503 387092003040 HypF finger; Region: zf-HYPF; pfam07503 387092003041 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 387092003042 Protein of unknown function (DUF328); Region: DUF328; cl01143 387092003043 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 387092003044 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 387092003045 High-affinity nickel-transport protein; Region: NicO; cl00964 387092003046 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 387092003047 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 387092003048 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 387092003049 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 387092003050 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 387092003051 dimerization interface [polypeptide binding]; other site 387092003052 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 387092003053 ATP binding site [chemical binding]; other site 387092003054 HypX protein, N-terminal hydrolase domain; Region: FMT_core_HypX_N; cd08650 387092003055 putative active site [active] 387092003056 putative substrate binding site [chemical binding]; other site 387092003057 putative cosubstrate binding site; other site 387092003058 catalytic site [active] 387092003059 C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins; Region: FMT_C_HypX; cd08701 387092003060 enoyl-CoA hydratase; Provisional; Region: PRK07659 387092003061 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 387092003062 substrate binding site [chemical binding]; other site 387092003063 oxyanion hole (OAH) forming residues; other site 387092003064 trimer interface [polypeptide binding]; other site 387092003065 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 387092003066 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 387092003067 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 387092003068 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 387092003069 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 387092003070 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 387092003071 active site 387092003072 DNA binding site [nucleotide binding] 387092003073 Int/Topo IB signature motif; other site 387092003074 Chorismate mutase type II; Region: CM_2; cl00693 387092003075 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 387092003076 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 387092003077 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 387092003078 ligand binding site [chemical binding]; other site 387092003079 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 387092003080 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 387092003081 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 387092003082 ligand binding site [chemical binding]; other site 387092003083 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 387092003084 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 387092003085 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 387092003086 Yqey-like protein; Region: YqeY; pfam09424 387092003087 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 387092003088 active site 387092003089 ribulose/triose binding site [chemical binding]; other site 387092003090 phosphate binding site [ion binding]; other site 387092003091 substrate (anthranilate) binding pocket [chemical binding]; other site 387092003092 product (indole) binding pocket [chemical binding]; other site 387092003093 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 387092003094 TPR motif; other site 387092003095 binding surface 387092003096 TPR repeat; Region: TPR_11; pfam13414 387092003097 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 387092003098 binding surface 387092003099 Tetratricopeptide repeat; Region: TPR_12; pfam13424 387092003100 TPR motif; other site 387092003101 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 387092003102 TPR motif; other site 387092003103 binding surface 387092003104 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 387092003105 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 387092003106 S-adenosylmethionine binding site [chemical binding]; other site 387092003107 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 387092003108 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 387092003109 Ligand binding site; other site 387092003110 oligomer interface; other site 387092003111 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 387092003112 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 387092003113 dimer interface [polypeptide binding]; other site 387092003114 conserved gate region; other site 387092003115 putative PBP binding loops; other site 387092003116 ABC-ATPase subunit interface; other site 387092003117 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 387092003118 argininosuccinate synthase; Provisional; Region: PRK13820 387092003119 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 387092003120 ANP binding site [chemical binding]; other site 387092003121 Substrate Binding Site II [chemical binding]; other site 387092003122 Substrate Binding Site I [chemical binding]; other site 387092003123 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 387092003124 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 387092003125 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 387092003126 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 387092003127 active site 387092003128 HslU subunit interaction site [polypeptide binding]; other site 387092003129 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 387092003130 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 387092003131 Walker A motif; other site 387092003132 ATP binding site [chemical binding]; other site 387092003133 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 387092003134 Walker B motif; other site 387092003135 arginine finger; other site 387092003136 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 387092003137 GTPase Era; Reviewed; Region: era; PRK00089 387092003138 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 387092003139 G1 box; other site 387092003140 GTP/Mg2+ binding site [chemical binding]; other site 387092003141 Switch I region; other site 387092003142 G2 box; other site 387092003143 Switch II region; other site 387092003144 G3 box; other site 387092003145 G4 box; other site 387092003146 G5 box; other site 387092003147 KH domain; Region: KH_2; pfam07650 387092003148 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 387092003149 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 387092003150 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 387092003151 AAA domain; Region: AAA_22; pfam13401 387092003152 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 387092003153 TPR repeat; Region: TPR_11; pfam13414 387092003154 TPR motif; other site 387092003155 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 387092003156 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 387092003157 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 387092003158 Walker A motif; other site 387092003159 ATP binding site [chemical binding]; other site 387092003160 Walker B motif; other site 387092003161 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 387092003162 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 387092003163 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 387092003164 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 387092003165 Part of AAA domain; Region: AAA_19; pfam13245 387092003166 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 387092003167 Family description; Region: UvrD_C_2; pfam13538 387092003168 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 387092003169 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387092003170 active site 387092003171 HIGH motif; other site 387092003172 nucleotide binding site [chemical binding]; other site 387092003173 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 387092003174 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 387092003175 active site 387092003176 KMSKS motif; other site 387092003177 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 387092003178 tRNA binding surface [nucleotide binding]; other site 387092003179 anticodon binding site; other site 387092003180 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 387092003181 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 387092003182 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 387092003183 Sulfate transporter family; Region: Sulfate_transp; pfam00916 387092003184 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 387092003185 dUTPase; Region: dUTPase_2; pfam08761 387092003186 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in dimeric 2-Deoxyuridine 5'-triphosphate nucleotidohydrolase and similar proteins; Region: NTP-PPase_dUTPase; cd11527 387092003187 active site 387092003188 homodimer interface [polypeptide binding]; other site 387092003189 metal binding site [ion binding]; metal-binding site 387092003190 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 387092003191 putative ABC transporter; Region: ycf24; CHL00085 387092003192 FeS assembly ATPase SufC; Region: sufC; TIGR01978 387092003193 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 387092003194 Walker A/P-loop; other site 387092003195 ATP binding site [chemical binding]; other site 387092003196 Q-loop/lid; other site 387092003197 ABC transporter signature motif; other site 387092003198 Walker B; other site 387092003199 D-loop; other site 387092003200 H-loop/switch region; other site 387092003201 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 387092003202 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 387092003203 Domain of unknown function DUF59; Region: DUF59; cl00941 387092003204 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 387092003205 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 387092003206 domain interfaces; other site 387092003207 active site 387092003208 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 387092003209 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 387092003210 phage T7 F exclusion suppressor FxsA; Reviewed; Region: fxsA; PRK11463 387092003211 prolyl-tRNA synthetase; Provisional; Region: PRK09194 387092003212 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 387092003213 dimer interface [polypeptide binding]; other site 387092003214 motif 1; other site 387092003215 active site 387092003216 motif 2; other site 387092003217 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 387092003218 putative deacylase active site [active] 387092003219 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 387092003220 active site 387092003221 motif 3; other site 387092003222 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 387092003223 anticodon binding site; other site 387092003224 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 387092003225 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 387092003226 tRNA; other site 387092003227 putative tRNA binding site [nucleotide binding]; other site 387092003228 putative NADP binding site [chemical binding]; other site 387092003229 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 387092003230 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 387092003231 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 387092003232 substrate binding pocket [chemical binding]; other site 387092003233 chain length determination region; other site 387092003234 substrate-Mg2+ binding site; other site 387092003235 catalytic residues [active] 387092003236 aspartate-rich region 1; other site 387092003237 active site lid residues [active] 387092003238 aspartate-rich region 2; other site 387092003239 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 387092003240 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 387092003241 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 387092003242 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 387092003243 S-adenosylmethionine binding site [chemical binding]; other site 387092003244 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 387092003245 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 387092003246 inhibitor-cofactor binding pocket; inhibition site 387092003247 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092003248 catalytic residue [active] 387092003249 SurA N-terminal domain; Region: SurA_N_3; cl07813 387092003250 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 387092003251 cell division protein FtsA; Region: ftsA; TIGR01174 387092003252 Cell division protein FtsA; Region: FtsA; smart00842 387092003253 Cell division protein FtsA; Region: FtsA; pfam14450 387092003254 cell division protein FtsZ; Validated; Region: PRK09330 387092003255 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 387092003256 nucleotide binding site [chemical binding]; other site 387092003257 SulA interaction site; other site 387092003258 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 387092003259 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 387092003260 Walker A/P-loop; other site 387092003261 ATP binding site [chemical binding]; other site 387092003262 Q-loop/lid; other site 387092003263 ABC transporter signature motif; other site 387092003264 Walker B; other site 387092003265 D-loop; other site 387092003266 H-loop/switch region; other site 387092003267 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 387092003268 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 387092003269 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 387092003270 S-adenosylmethionine binding site [chemical binding]; other site 387092003271 Peptidase family M48; Region: Peptidase_M48; pfam01435 387092003272 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 387092003273 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092003274 Walker A/P-loop; other site 387092003275 ATP binding site [chemical binding]; other site 387092003276 Q-loop/lid; other site 387092003277 ABC transporter signature motif; other site 387092003278 Walker B; other site 387092003279 D-loop; other site 387092003280 H-loop/switch region; other site 387092003281 ABC transporter; Region: ABC_tran_2; pfam12848 387092003282 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 387092003283 Thermotoga maritima CorA-like family; Region: TmCorA-like; cd12822 387092003284 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 387092003285 oligomer interface [polypeptide binding]; other site 387092003286 metal binding site [ion binding]; metal-binding site 387092003287 metal binding site [ion binding]; metal-binding site 387092003288 putative Cl binding site [ion binding]; other site 387092003289 aspartate ring; other site 387092003290 basic sphincter; other site 387092003291 hydrophobic gate; other site 387092003292 periplasmic entrance; other site 387092003293 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 387092003294 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 387092003295 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092003296 catalytic residue [active] 387092003297 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 387092003298 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 387092003299 feedback inhibition sensing region; other site 387092003300 homohexameric interface [polypeptide binding]; other site 387092003301 nucleotide binding site [chemical binding]; other site 387092003302 N-acetyl-L-glutamate binding site [chemical binding]; other site 387092003303 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 387092003304 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 387092003305 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 387092003306 inhibitor-cofactor binding pocket; inhibition site 387092003307 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092003308 catalytic residue [active] 387092003309 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 387092003310 dinuclear metal binding motif [ion binding]; other site 387092003311 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 387092003312 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; cd03440 387092003313 active site 2 [active] 387092003314 active site 1 [active] 387092003315 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 387092003316 ArsC family; Region: ArsC; pfam03960 387092003317 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 387092003318 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 387092003319 active site 387092003320 motif I; other site 387092003321 motif II; other site 387092003322 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 387092003323 Methyltransferase domain; Region: Methyltransf_23; pfam13489 387092003324 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 387092003325 S-adenosylmethionine binding site [chemical binding]; other site 387092003326 nucleosidase; Provisional; Region: PRK05634 387092003327 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 387092003328 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 387092003329 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 387092003330 phosphodiesterase; Provisional; Region: PRK12704 387092003331 Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; Region: iSH2_PI3K_IA_R; cl17108 387092003332 heterodimer interface [polypeptide binding]; other site 387092003333 KH domain; Region: KH_1; pfam00013 387092003334 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 387092003335 Zn2+ binding site [ion binding]; other site 387092003336 Mg2+ binding site [ion binding]; other site 387092003337 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 387092003338 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 387092003339 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 387092003340 catalytic residues [active] 387092003341 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 387092003342 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 387092003343 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 387092003344 P loop; other site 387092003345 GTP binding site [chemical binding]; other site 387092003346 DNA repair protein RadA; Provisional; Region: PRK11823 387092003347 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 387092003348 Walker A motif; other site 387092003349 ATP binding site [chemical binding]; other site 387092003350 Walker B motif; other site 387092003351 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 387092003352 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 387092003353 Permease; Region: Permease; pfam02405 387092003354 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 387092003355 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 387092003356 thiS-thiF/thiG interaction site; other site 387092003357 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 387092003358 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 387092003359 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 387092003360 Uncharacterized conserved protein [Function unknown]; Region: COG1565 387092003361 Outer membrane efflux protein; Region: OEP; pfam02321 387092003362 Outer membrane efflux protein; Region: OEP; pfam02321 387092003363 acetylornithine aminotransferase; Provisional; Region: PRK02627 387092003364 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 387092003365 inhibitor-cofactor binding pocket; inhibition site 387092003366 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092003367 catalytic residue [active] 387092003368 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 387092003369 metal binding triad [ion binding]; metal-binding site 387092003370 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 387092003371 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 387092003372 molybdopterin cofactor binding site; other site 387092003373 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cd02775 387092003374 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092003375 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 387092003376 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 387092003377 Walker A motif; other site 387092003378 ATP binding site [chemical binding]; other site 387092003379 Walker B motif; other site 387092003380 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 387092003381 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 387092003382 Walker A motif; other site 387092003383 ATP binding site [chemical binding]; other site 387092003384 Walker B motif; other site 387092003385 Peptidase family M41; Region: Peptidase_M41; pfam01434 387092003386 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 387092003387 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 387092003388 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_A; cd01570 387092003389 active site 387092003390 Pseudogene. Similar to pyrazinamidase/nicotinamidase PncA. This CDS appears to have a frameshift mutation following codon 57. 387092003391 Probable gene remnant. Similar to the N-terminal region of Aquifex aeolicus VF5 pyrazinamidase/nicotinamidase PncA (198 aa) aq_994. 387092003392 Probable gene remnant. Similar to the C-terminal region of Aquifex aeolicus VF5 pyrazinamidase/nicotinamidase PncA (198 aa) aq_994. 387092003393 S-adenosylmethionine synthetase; Validated; Region: PRK05250 387092003394 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 387092003395 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 387092003396 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 387092003397 Response regulator receiver domain; Region: Response_reg; pfam00072 387092003398 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092003399 active site 387092003400 phosphorylation site [posttranslational modification] 387092003401 intermolecular recognition site; other site 387092003402 dimerization interface [polypeptide binding]; other site 387092003403 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092003404 metal binding site [ion binding]; metal-binding site 387092003405 active site 387092003406 I-site; other site 387092003407 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 387092003408 Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]; Region: CheB; COG2201 387092003409 CheB methylesterase; Region: CheB_methylest; pfam01339 387092003410 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 387092003411 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 387092003412 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 387092003413 PAS domain; Region: PAS_10; pfam13596 387092003414 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 387092003415 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092003416 ATP binding site [chemical binding]; other site 387092003417 Mg2+ binding site [ion binding]; other site 387092003418 G-X-G motif; other site 387092003419 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 387092003420 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 387092003421 metal binding site 2 [ion binding]; metal-binding site 387092003422 putative DNA binding helix; other site 387092003423 metal binding site 1 [ion binding]; metal-binding site 387092003424 dimer interface [polypeptide binding]; other site 387092003425 structural Zn2+ binding site [ion binding]; other site 387092003426 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 387092003427 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 387092003428 Walker B motif; other site 387092003429 arginine finger; other site 387092003430 Peptidase family M41; Region: Peptidase_M41; pfam01434 387092003431 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 387092003432 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 387092003433 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 387092003434 FeS/SAM binding site; other site 387092003435 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 387092003436 Mechanosensitive ion channel; Region: MS_channel; pfam00924 387092003437 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 387092003438 active site 387092003439 dimer interface [polypeptide binding]; other site 387092003440 metal binding site [ion binding]; metal-binding site 387092003441 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 387092003442 TrkA-C domain; Region: TrkA_C; pfam02080 387092003443 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 387092003444 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 387092003445 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 387092003446 active site 387092003447 hydrophilic channel; other site 387092003448 dimerization interface [polypeptide binding]; other site 387092003449 catalytic residues [active] 387092003450 active site lid [active] 387092003451 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 387092003452 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 387092003453 Domain of unknown function DUF77; Region: DUF77; pfam01910 387092003454 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 387092003455 homodimer interface [polypeptide binding]; other site 387092003456 oligomer interface [polypeptide binding]; other site 387092003457 chemical substrate binding site [chemical binding]; other site 387092003458 metal binding site [ion binding]; metal-binding site 387092003459 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 387092003460 nucleotide binding site/active site [active] 387092003461 HIT family signature motif; other site 387092003462 catalytic residue [active] 387092003463 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 387092003464 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 387092003465 DctM-like transporters; Region: DctM; pfam06808 387092003466 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 387092003467 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 387092003468 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 387092003469 Predicted membrane protein [Function unknown]; Region: COG2860 387092003470 UPF0126 domain; Region: UPF0126; pfam03458 387092003471 UPF0126 domain; Region: UPF0126; pfam03458 387092003472 HI0933-like protein; Region: HI0933_like; pfam03486 387092003473 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 387092003474 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 387092003475 ATP-grasp domain; Region: ATP-grasp_4; cl17255 387092003476 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 387092003477 RuvA N terminal domain; Region: RuvA_N; pfam01330 387092003478 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 387092003479 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 387092003480 Major Facilitator Superfamily; Region: MFS_1; pfam07690 387092003481 putative substrate translocation pore; other site 387092003482 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 387092003483 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 387092003484 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 387092003485 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 387092003486 active site 387092003487 HIGH motif; other site 387092003488 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 387092003489 KMSKS motif; other site 387092003490 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 387092003491 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 387092003492 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 387092003493 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092003494 Walker A/P-loop; other site 387092003495 ATP binding site [chemical binding]; other site 387092003496 Q-loop/lid; other site 387092003497 ABC transporter signature motif; other site 387092003498 Walker B; other site 387092003499 D-loop; other site 387092003500 H-loop/switch region; other site 387092003501 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 387092003502 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 387092003503 Substrate binding site; other site 387092003504 Mg++ binding site; other site 387092003505 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 387092003506 active site 387092003507 substrate binding site [chemical binding]; other site 387092003508 CoA binding site [chemical binding]; other site 387092003509 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 387092003510 Flavoprotein; Region: Flavoprotein; pfam02441 387092003511 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 387092003512 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 387092003513 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 387092003514 catalytic residue [active] 387092003515 putative FPP diphosphate binding site; other site 387092003516 putative FPP binding hydrophobic cleft; other site 387092003517 dimer interface [polypeptide binding]; other site 387092003518 putative IPP diphosphate binding site; other site 387092003519 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 387092003520 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 387092003521 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 387092003522 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 387092003523 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 387092003524 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 387092003525 dimerization interface 3.5A [polypeptide binding]; other site 387092003526 active site 387092003527 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 387092003528 putative ligand binding pocket/active site [active] 387092003529 putative metal binding site [ion binding]; other site 387092003530 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 387092003531 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 387092003532 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 387092003533 active site 387092003534 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 387092003535 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 387092003536 Ligand binding site; other site 387092003537 Putative Catalytic site; other site 387092003538 DXD motif; other site 387092003539 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 387092003540 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 387092003541 dihydroorotase; Provisional; Region: PRK08417 387092003542 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 387092003543 active site 387092003544 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 387092003545 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 387092003546 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 387092003547 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 387092003548 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 387092003549 DsbD alpha interface [polypeptide binding]; other site 387092003550 catalytic residues [active] 387092003551 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 387092003552 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein; Region: SSP411; cd02955 387092003553 catalytic residues [active] 387092003554 methionine sulfoxide reductase A; Provisional; Region: PRK14054 387092003555 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 387092003556 putative active site [active] 387092003557 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 387092003558 dimerization interface [polypeptide binding]; other site 387092003559 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 387092003560 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092003561 dimer interface [polypeptide binding]; other site 387092003562 putative CheW interface [polypeptide binding]; other site 387092003563 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 387092003564 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 387092003565 nucleotide binding site [chemical binding]; other site 387092003566 NEF interaction site [polypeptide binding]; other site 387092003567 SBD interface [polypeptide binding]; other site 387092003568 GrpE; Region: GrpE; pfam01025 387092003569 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 387092003570 dimer interface [polypeptide binding]; other site 387092003571 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 387092003572 heat-inducible transcription repressor; Provisional; Region: PRK03911 387092003573 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 387092003574 16S/18S rRNA binding site [nucleotide binding]; other site 387092003575 S13e-L30e interaction site [polypeptide binding]; other site 387092003576 25S rRNA binding site [nucleotide binding]; other site 387092003577 Helix-turn-helix domain; Region: HTH_28; pfam13518 387092003578 putative transposase OrfB; Reviewed; Region: PHA02517 387092003579 Homeodomain-like domain; Region: HTH_32; pfam13565 387092003580 Integrase core domain; Region: rve; pfam00665 387092003581 Integrase core domain; Region: rve_3; pfam13683 387092003582 Rrf2 family protein; Region: rrf2_super; TIGR00738 387092003583 Transcriptional regulator; Region: Rrf2; pfam02082 387092003584 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 387092003585 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092003586 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092003587 metal binding site [ion binding]; metal-binding site 387092003588 active site 387092003589 I-site; other site 387092003590 Methyltransferase domain; Region: Methyltransf_31; pfam13847 387092003591 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 387092003592 S-adenosylmethionine binding site [chemical binding]; other site 387092003593 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 387092003594 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein; Region: SSP411; cd02955 387092003595 catalytic residues [active] 387092003596 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 387092003597 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387092003598 active site 387092003599 nucleotide binding site [chemical binding]; other site 387092003600 HIGH motif; other site 387092003601 KMSKS motif; other site 387092003602 Riboflavin kinase; Region: Flavokinase; smart00904 387092003603 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 387092003604 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 387092003605 RNA binding surface [nucleotide binding]; other site 387092003606 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 387092003607 S-adenosylmethionine binding site [chemical binding]; other site 387092003608 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 387092003609 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 387092003610 nucleotide binding pocket [chemical binding]; other site 387092003611 K-X-D-G motif; other site 387092003612 catalytic site [active] 387092003613 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 387092003614 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 387092003615 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo...; Region: BRCT; cd00027 387092003616 Dimer interface [polypeptide binding]; other site 387092003617 BRCT sequence motif; other site 387092003618 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092003619 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092003620 metal binding site [ion binding]; metal-binding site 387092003621 active site 387092003622 I-site; other site 387092003623 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 387092003624 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 387092003625 Cytochrome c; Region: Cytochrom_C; pfam00034 387092003626 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 387092003627 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 387092003628 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 387092003629 putative RNA binding site [nucleotide binding]; other site 387092003630 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 387092003631 S-adenosylmethionine binding site [chemical binding]; other site 387092003632 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 387092003633 dihydropteroate synthase; Region: DHPS; TIGR01496 387092003634 substrate binding pocket [chemical binding]; other site 387092003635 dimer interface [polypeptide binding]; other site 387092003636 inhibitor binding site; inhibition site 387092003637 DNA polymerase III subunit delta'; Validated; Region: PRK08485 387092003638 DNA replication regulator; Region: HobA; pfam12163 387092003639 aspartate kinase; Reviewed; Region: PRK06635 387092003640 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 387092003641 putative nucleotide binding site [chemical binding]; other site 387092003642 putative catalytic residues [active] 387092003643 putative Mg ion binding site [ion binding]; other site 387092003644 putative aspartate binding site [chemical binding]; other site 387092003645 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 387092003646 putative allosteric regulatory site; other site 387092003647 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 387092003648 putative allosteric regulatory residue; other site 387092003649 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 387092003650 putative active site [active] 387092003651 Ap4A binding site [chemical binding]; other site 387092003652 nudix motif; other site 387092003653 putative metal binding site [ion binding]; other site 387092003654 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 387092003655 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 387092003656 FeS/SAM binding site; other site 387092003657 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 387092003658 sec-independent translocase; Provisional; Region: PRK04098 387092003659 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 387092003660 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 387092003661 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 387092003662 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 387092003663 catalytic core [active] 387092003664 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 387092003665 putative catalytic site [active] 387092003666 putative phosphate binding site [ion binding]; other site 387092003667 active site 387092003668 metal binding site A [ion binding]; metal-binding site 387092003669 DNA binding site [nucleotide binding] 387092003670 putative AP binding site [nucleotide binding]; other site 387092003671 putative metal binding site B [ion binding]; other site 387092003672 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 387092003673 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 387092003674 Cl- selectivity filter; other site 387092003675 Cl- binding residues [ion binding]; other site 387092003676 pore gating glutamate residue; other site 387092003677 dimer interface [polypeptide binding]; other site 387092003678 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 387092003679 metal binding site 2 [ion binding]; metal-binding site 387092003680 putative DNA binding helix; other site 387092003681 metal binding site 1 [ion binding]; metal-binding site 387092003682 dimer interface [polypeptide binding]; other site 387092003683 structural Zn2+ binding site [ion binding]; other site 387092003684 DPS-like protein, ferritin-like diiron-binding domain; Region: DPSL; cd01052 387092003685 Ferritin-like domain; Region: Ferritin; pfam00210 387092003686 diiron binding motif [ion binding]; other site 387092003687 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 387092003688 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 387092003689 active site residue [active] 387092003690 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 387092003691 active site residue [active] 387092003692 YceI-like domain; Region: YceI; cl01001 387092003693 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 387092003694 ABC1 family; Region: ABC1; cl17513 387092003695 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 387092003696 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 387092003697 protein binding site [polypeptide binding]; other site 387092003698 DNA protecting protein DprA; Region: dprA; TIGR00732 387092003699 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 387092003700 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 387092003701 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 387092003702 transmembrane helices; other site 387092003703 phage lambda Rz-like lysis protein; Region: PHA00276 387092003704 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 387092003705 NodB motif; other site 387092003706 putative active site [active] 387092003707 putative catalytic site [active] 387092003708 Zn binding site [ion binding]; other site 387092003709 ketol-acid reductoisomerase; Provisional; Region: PRK05479 387092003710 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 387092003711 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 387092003712 Exoribonuclease R [Transcription]; Region: VacB; COG0557 387092003713 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 387092003714 RNB domain; Region: RNB; pfam00773 387092003715 DNA polymerase III subunit delta; Validated; Region: PRK08487 387092003716 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 387092003717 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 387092003718 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 387092003719 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 387092003720 dimer interface [polypeptide binding]; other site 387092003721 ssDNA binding site [nucleotide binding]; other site 387092003722 tetramer (dimer of dimers) interface [polypeptide binding]; other site 387092003723 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 387092003724 HDOD domain; Region: HDOD; pfam08668 387092003725 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 387092003726 S-adenosylmethionine binding site [chemical binding]; other site 387092003727 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 387092003728 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 387092003729 pantothenate kinase; Reviewed; Region: PRK13333 387092003730 PQQ-like domain; Region: PQQ_2; pfam13360 387092003731 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 387092003732 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 387092003733 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 387092003734 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 387092003735 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 387092003736 Walker A motif; other site 387092003737 ATP binding site [chemical binding]; other site 387092003738 Walker B motif; other site 387092003739 Colicin V production protein; Region: Colicin_V; pfam02674 387092003740 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 387092003741 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 387092003742 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 387092003743 dimer interface [polypeptide binding]; other site 387092003744 putative anticodon binding site; other site 387092003745 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 387092003746 motif 1; other site 387092003747 active site 387092003748 motif 2; other site 387092003749 motif 3; other site 387092003750 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 387092003751 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 387092003752 dimer interface [polypeptide binding]; other site 387092003753 active site 387092003754 glycine-pyridoxal phosphate binding site [chemical binding]; other site 387092003755 folate binding site [chemical binding]; other site 387092003756 Sporulation related domain; Region: SPOR; pfam05036 387092003757 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 387092003758 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 387092003759 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 387092003760 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 387092003761 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 387092003762 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 387092003763 shikimate binding site; other site 387092003764 NAD(P) binding site [chemical binding]; other site 387092003765 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 387092003766 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 387092003767 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092003768 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092003769 metal binding site [ion binding]; metal-binding site 387092003770 active site 387092003771 I-site; other site 387092003772 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 387092003773 active site residue [active] 387092003774 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 387092003775 recombination protein RecR; Reviewed; Region: recR; PRK00076 387092003776 RecR protein; Region: RecR; pfam02132 387092003777 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 387092003778 putative active site [active] 387092003779 putative metal-binding site [ion binding]; other site 387092003780 tetramer interface [polypeptide binding]; other site 387092003781 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 387092003782 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 387092003783 HSP70 interaction site [polypeptide binding]; other site 387092003784 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 387092003785 substrate binding site [polypeptide binding]; other site 387092003786 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 387092003787 Zn binding sites [ion binding]; other site 387092003788 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 387092003789 dimer interface [polypeptide binding]; other site 387092003790 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 387092003791 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 387092003792 DNA polymerase I; Provisional; Region: PRK05755 387092003793 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 387092003794 active site 387092003795 metal binding site 1 [ion binding]; metal-binding site 387092003796 putative 5' ssDNA interaction site; other site 387092003797 metal binding site 3; metal-binding site 387092003798 metal binding site 2 [ion binding]; metal-binding site 387092003799 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 387092003800 putative DNA binding site [nucleotide binding]; other site 387092003801 putative metal binding site [ion binding]; other site 387092003802 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 387092003803 active site 387092003804 catalytic site [active] 387092003805 substrate binding site [chemical binding]; other site 387092003806 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 387092003807 active site 387092003808 DNA binding site [nucleotide binding] 387092003809 catalytic site [active] 387092003810 HDOD domain; Region: HDOD; pfam08668 387092003811 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 387092003812 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 387092003813 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 387092003814 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 387092003815 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 387092003816 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 387092003817 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 387092003818 FMN binding site [chemical binding]; other site 387092003819 active site 387092003820 catalytic residues [active] 387092003821 substrate binding site [chemical binding]; other site 387092003822 Membrane-associating domain; Region: MARVEL; pfam01284 387092003823 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 387092003824 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 387092003825 thiamine phosphate binding site [chemical binding]; other site 387092003826 active site 387092003827 pyrophosphate binding site [ion binding]; other site 387092003828 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 387092003829 RNA polymerases M/15 Kd subunit; Region: RNA_POL_M_15KD; cl02717 387092003830 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 387092003831 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 387092003832 active site 387092003833 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 387092003834 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 387092003835 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 387092003836 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 387092003837 active site 387092003838 dimer interface [polypeptide binding]; other site 387092003839 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 387092003840 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 387092003841 active site 387092003842 FMN binding site [chemical binding]; other site 387092003843 substrate binding site [chemical binding]; other site 387092003844 3Fe-4S cluster binding site [ion binding]; other site 387092003845 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 387092003846 domain interface; other site 387092003847 putative recombination protein RecO; Provisional; Region: PRK13908 387092003848 CheW-like domain; Region: CheW; pfam01584 387092003849 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 387092003850 CheW-like domain; Region: CheW; pfam01584 387092003851 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 387092003852 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 387092003853 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092003854 dimer interface [polypeptide binding]; other site 387092003855 putative CheW interface [polypeptide binding]; other site 387092003856 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092003857 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092003858 metal binding site [ion binding]; metal-binding site 387092003859 active site 387092003860 I-site; other site 387092003861 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 387092003862 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 387092003863 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 387092003864 Ligand Binding Site [chemical binding]; other site 387092003865 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 387092003866 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 387092003867 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 387092003868 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 387092003869 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 387092003870 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 387092003871 Transcription factor/nuclear export subunit protein 2; Region: Tho2; pfam11262 387092003872 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 387092003873 binding surface 387092003874 TPR motif; other site 387092003875 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 387092003876 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 387092003877 ligand binding site [chemical binding]; other site 387092003878 translocation protein TolB; Provisional; Region: tolB; PRK04043 387092003879 TonB C terminal; Region: TonB_2; pfam13103 387092003880 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 387092003881 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 387092003882 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 387092003883 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 387092003884 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 387092003885 gamma subunit interface [polypeptide binding]; other site 387092003886 epsilon subunit interface [polypeptide binding]; other site 387092003887 LBP interface [polypeptide binding]; other site 387092003888 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 387092003889 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 387092003890 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 387092003891 alpha subunit interaction interface [polypeptide binding]; other site 387092003892 Walker A motif; other site 387092003893 ATP binding site [chemical binding]; other site 387092003894 Walker B motif; other site 387092003895 inhibitor binding site; inhibition site 387092003896 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 387092003897 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 387092003898 core domain interface [polypeptide binding]; other site 387092003899 delta subunit interface [polypeptide binding]; other site 387092003900 epsilon subunit interface [polypeptide binding]; other site 387092003901 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 387092003902 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 387092003903 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 387092003904 beta subunit interaction interface [polypeptide binding]; other site 387092003905 Walker A motif; other site 387092003906 ATP binding site [chemical binding]; other site 387092003907 Walker B motif; other site 387092003908 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 387092003909 F0F1 ATP synthase subunit delta; Validated; Region: PRK08474 387092003910 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 387092003911 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 387092003912 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 387092003913 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 387092003914 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 387092003915 ParB-like nuclease domain; Region: ParB; smart00470 387092003916 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 387092003917 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 387092003918 P-loop; other site 387092003919 Magnesium ion binding site [ion binding]; other site 387092003920 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 387092003921 biotin--protein ligase; Provisional; Region: PRK08477 387092003922 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 387092003923 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 387092003924 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 387092003925 putative active site [active] 387092003926 substrate binding site [chemical binding]; other site 387092003927 putative cosubstrate binding site; other site 387092003928 catalytic site [active] 387092003929 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 387092003930 substrate binding site [chemical binding]; other site 387092003931 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 387092003932 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 387092003933 active site 387092003934 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 387092003935 nucleotide binding site [chemical binding]; other site 387092003936 homotetrameric interface [polypeptide binding]; other site 387092003937 putative phosphate binding site [ion binding]; other site 387092003938 putative allosteric binding site; other site 387092003939 GTPase CgtA; Reviewed; Region: obgE; PRK12299 387092003940 GTP1/OBG; Region: GTP1_OBG; pfam01018 387092003941 Obg GTPase; Region: Obg; cd01898 387092003942 G1 box; other site 387092003943 GTP/Mg2+ binding site [chemical binding]; other site 387092003944 Switch I region; other site 387092003945 G2 box; other site 387092003946 G3 box; other site 387092003947 Switch II region; other site 387092003948 G4 box; other site 387092003949 G5 box; other site 387092003950 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 387092003951 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 387092003952 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 387092003953 homotrimer interaction site [polypeptide binding]; other site 387092003954 putative active site [active] 387092003955 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 387092003956 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 387092003957 metal binding site [ion binding]; metal-binding site 387092003958 dimer interface [polypeptide binding]; other site 387092003959 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 387092003960 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 387092003961 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 387092003962 cytochrome c nitrite reductase, pentaheme subunit; Region: cyt_nit_nrfB; TIGR03146 387092003963 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 387092003964 catalytic residues [active] 387092003965 DNA helicase, putative; Region: TIGR00376 387092003966 Part of AAA domain; Region: AAA_19; pfam13245 387092003967 AAA domain; Region: AAA_12; pfam13087 387092003968 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 387092003969 Pseudogene. Similar to UDP-glucose 4-epimerase. This CDS is disrupted by the insertion of IS element following codon 174. 387092003970 Probable gene remnant. Similar to the C-terminal region of Campylobacter lari RM2100 UDP-glucose 4-epimerase (328 aa) CLA0439. 387092003971 IS2 transposase TnpB; Reviewed; Region: PRK09409 387092003972 HTH-like domain; Region: HTH_21; pfam13276 387092003973 Integrase core domain; Region: rve; pfam00665 387092003974 Integrase core domain; Region: rve_3; pfam13683 387092003975 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 387092003976 Transposase; Region: HTH_Tnp_1; cl17663 387092003977 Probable gene remnant. Similar to the N-terminal region of Campylobacter lari RM2100 UDP-glucose 4-epimerase (328 aa) CLA0439. 387092003978 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 387092003979 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 387092003980 NAD(P) binding site [chemical binding]; other site 387092003981 homodimer interface [polypeptide binding]; other site 387092003982 substrate binding site [chemical binding]; other site 387092003983 active site 387092003984 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 387092003985 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 387092003986 inhibitor-cofactor binding pocket; inhibition site 387092003987 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092003988 catalytic residue [active] 387092003989 Bacterial sugar transferase; Region: Bac_transf; pfam02397 387092003990 Oligosaccharyl transferase STT3 subunit; Region: STT3; pfam02516 387092003991 ExoA is involved in the biosynthesis of succinoglycan; Region: Succinoglycan_BP_ExoA; cd02525 387092003992 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 387092003993 Ligand binding site; other site 387092003994 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 387092003995 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 387092003996 putative active site [active] 387092003997 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 387092003998 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 387092003999 Polysaccharide biosynthesis protein; Region: Polysacc_synt_3; pfam13440 387092004000 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 387092004001 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 387092004002 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387092004003 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 387092004004 active site 387092004005 nucleotide binding site [chemical binding]; other site 387092004006 HIGH motif; other site 387092004007 KMSKS motif; other site 387092004008 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cd00688 387092004009 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 387092004010 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 387092004011 Methyltransferase domain; Region: Methyltransf_31; pfam13847 387092004012 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 387092004013 S-adenosylmethionine binding site [chemical binding]; other site 387092004014 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 387092004015 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 387092004016 active site 387092004017 homodimer interface [polypeptide binding]; other site 387092004018 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; Region: UDPG_MGDP_dh_N; pfam03721 387092004019 prephenate dehydrogenase; Validated; Region: PRK08507 387092004020 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 387092004021 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 387092004022 MutS domain III; Region: MutS_III; pfam05192 387092004023 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092004024 Walker A/P-loop; other site 387092004025 ATP binding site [chemical binding]; other site 387092004026 Q-loop/lid; other site 387092004027 ABC transporter signature motif; other site 387092004028 Walker B; other site 387092004029 D-loop; other site 387092004030 H-loop/switch region; other site 387092004031 Smr domain; Region: Smr; pfam01713 387092004032 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 387092004033 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 387092004034 active site 387092004035 NTP binding site [chemical binding]; other site 387092004036 metal binding triad [ion binding]; metal-binding site 387092004037 antibiotic binding site [chemical binding]; other site 387092004038 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 387092004039 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 387092004040 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 387092004041 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 387092004042 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 387092004043 metal binding triad [ion binding]; metal-binding site 387092004044 hypothetical protein; Provisional; Region: PRK05839 387092004045 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 387092004046 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092004047 homodimer interface [polypeptide binding]; other site 387092004048 catalytic residue [active] 387092004049 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 387092004050 putative active site [active] 387092004051 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cl17196 387092004052 thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily; Region: adenyl_thiF; TIGR02356 387092004053 ATP binding site [chemical binding]; other site 387092004054 substrate interface [chemical binding]; other site 387092004055 Predicted amidohydrolase [General function prediction only]; Region: COG0388 387092004056 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 387092004057 active site 387092004058 catalytic triad [active] 387092004059 dimer interface [polypeptide binding]; other site 387092004060 Exonuclease VII small subunit; Region: Exonuc_VII_S; pfam02609 387092004061 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 387092004062 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 387092004063 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 387092004064 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 387092004065 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 387092004066 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 387092004067 homodimer interface [polypeptide binding]; other site 387092004068 substrate-cofactor binding pocket; other site 387092004069 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092004070 catalytic residue [active] 387092004071 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 387092004072 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 387092004073 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 387092004074 catalytic residue [active] 387092004075 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 387092004076 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 387092004077 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 387092004078 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 387092004079 active site 387092004080 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 387092004081 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 387092004082 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 387092004083 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 387092004084 active site 387092004085 HIGH motif; other site 387092004086 nucleotide binding site [chemical binding]; other site 387092004087 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 387092004088 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 387092004089 active site 387092004090 KMSKS motif; other site 387092004091 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 387092004092 tRNA binding surface [nucleotide binding]; other site 387092004093 anticodon binding site; other site 387092004094 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 387092004095 Competence-damaged protein; Region: CinA; pfam02464 387092004096 PilZ domain; Region: PilZ; pfam07238 387092004097 PilZ domain; Region: PilZ; pfam07238 387092004098 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 387092004099 nudix motif; other site 387092004100 hypothetical protein; Provisional; Region: PRK08609 387092004101 Nucleotidyltransferase (NT) domain of family X DNA Polymerases; Region: NT_POLXc; cd00141 387092004102 active site 387092004103 primer binding site [nucleotide binding]; other site 387092004104 NTP binding site [chemical binding]; other site 387092004105 metal binding triad [ion binding]; metal-binding site 387092004106 Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; Region: PHP_PolX; cd07436 387092004107 active site 387092004108 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092004109 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092004110 active site 387092004111 phosphorylation site [posttranslational modification] 387092004112 intermolecular recognition site; other site 387092004113 dimerization interface [polypeptide binding]; other site 387092004114 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 387092004115 DNA binding site [nucleotide binding] 387092004116 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092004117 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 387092004118 dimer interface [polypeptide binding]; other site 387092004119 phosphorylation site [posttranslational modification] 387092004120 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092004121 ATP binding site [chemical binding]; other site 387092004122 Mg2+ binding site [ion binding]; other site 387092004123 G-X-G motif; other site 387092004124 Cytochrome c; Region: Cytochrom_C; cl11414 387092004125 thioredoxin 2; Provisional; Region: PRK10996 387092004126 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 387092004127 catalytic residues [active] 387092004128 Cytochrome c; Region: Cytochrom_C; pfam00034 387092004129 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 387092004130 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387092004131 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 387092004132 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 387092004133 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 387092004134 dimer interface [polypeptide binding]; other site 387092004135 active site 387092004136 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 387092004137 catalytic residues [active] 387092004138 substrate binding site [chemical binding]; other site 387092004139 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 387092004140 Chlamydia CHLPS protein (DUF818); Region: DUF818; pfam05677 387092004141 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 387092004142 trimerization site [polypeptide binding]; other site 387092004143 active site 387092004144 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 387092004145 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]; Region: COG5016 387092004146 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 387092004147 active site 387092004148 catalytic residues [active] 387092004149 metal binding site [ion binding]; metal-binding site 387092004150 homodimer binding site [polypeptide binding]; other site 387092004151 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 387092004152 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 387092004153 carboxyltransferase (CT) interaction site; other site 387092004154 biotinylation site [posttranslational modification]; other site 387092004155 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; pfam04277 387092004156 Methyltransferase domain; Region: Methyltransf_23; pfam13489 387092004157 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 387092004158 S-adenosylmethionine binding site [chemical binding]; other site 387092004159 Protein of unknown function DUF72; Region: DUF72; pfam01904 387092004160 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 387092004161 substrate binding site [chemical binding]; other site 387092004162 phosphoserine phosphatase SerB; Region: serB; TIGR00338 387092004163 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 387092004164 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 387092004165 motif II; other site 387092004166 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 387092004167 FAD binding site [chemical binding]; other site 387092004168 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 387092004169 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 387092004170 putative active site [active] 387092004171 putative metal binding site [ion binding]; other site 387092004172 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 387092004173 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 387092004174 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 387092004175 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 387092004176 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 387092004177 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 387092004178 Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]; Region: LpxB; COG0763 387092004179 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 387092004180 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 387092004181 inhibitor-cofactor binding pocket; inhibition site 387092004182 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092004183 catalytic residue [active] 387092004184 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 387092004185 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 387092004186 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 387092004187 Membrane transport protein; Region: Mem_trans; cl09117 387092004188 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 387092004189 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 387092004190 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 387092004191 putative ATP binding site [chemical binding]; other site 387092004192 putative substrate interface [chemical binding]; other site 387092004193 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 387092004194 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 387092004195 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 387092004196 CHC2 zinc finger; Region: zf-CHC2; cl17510 387092004197 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 387092004198 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 387092004199 integrase; Provisional; Region: PRK09692 387092004200 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 387092004201 active site 387092004202 Int/Topo IB signature motif; other site 387092004203 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 387092004204 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 387092004205 oligomer interface [polypeptide binding]; other site 387092004206 RNA binding site [nucleotide binding]; other site 387092004207 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 387092004208 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 387092004209 oligomer interface [polypeptide binding]; other site 387092004210 RNA binding site [nucleotide binding]; other site 387092004211 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 387092004212 putative nucleic acid binding region [nucleotide binding]; other site 387092004213 G-X-X-G motif; other site 387092004214 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 387092004215 RNA binding site [nucleotide binding]; other site 387092004216 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 387092004217 HSP70 interaction site [polypeptide binding]; other site 387092004218 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 387092004219 mce related protein; Region: MCE; pfam02470 387092004220 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 387092004221 Organic solvent tolerance protein; Region: OstA_C; pfam04453 387092004222 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 387092004223 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 387092004224 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 387092004225 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 387092004226 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 387092004227 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 387092004228 active site 387092004229 GMP synthase; Reviewed; Region: guaA; PRK00074 387092004230 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 387092004231 AMP/PPi binding site [chemical binding]; other site 387092004232 candidate oxyanion hole; other site 387092004233 catalytic triad [active] 387092004234 potential glutamine specificity residues [chemical binding]; other site 387092004235 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 387092004236 ATP Binding subdomain [chemical binding]; other site 387092004237 Ligand Binding sites [chemical binding]; other site 387092004238 Dimerization subdomain; other site 387092004239 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 387092004240 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 387092004241 L-aspartate oxidase; Provisional; Region: PRK06175 387092004242 Aspartate oxidase [Coenzyme metabolism]; Region: NadB; COG0029 387092004243 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 387092004244 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 387092004245 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 387092004246 GIY-YIG motif/motif A; other site 387092004247 active site 387092004248 catalytic site [active] 387092004249 putative DNA binding site [nucleotide binding]; other site 387092004250 metal binding site [ion binding]; metal-binding site 387092004251 UvrB/uvrC motif; Region: UVR; pfam02151 387092004252 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 387092004253 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 387092004254 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 387092004255 Nitrate and nitrite sensing; Region: NIT; pfam08376 387092004256 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 387092004257 dimer interface [polypeptide binding]; other site 387092004258 phosphorylation site [posttranslational modification] 387092004259 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092004260 ATP binding site [chemical binding]; other site 387092004261 Mg2+ binding site [ion binding]; other site 387092004262 G-X-G motif; other site 387092004263 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 387092004264 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092004265 active site 387092004266 phosphorylation site [posttranslational modification] 387092004267 intermolecular recognition site; other site 387092004268 dimerization interface [polypeptide binding]; other site 387092004269 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 387092004270 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092004271 active site 387092004272 phosphorylation site [posttranslational modification] 387092004273 intermolecular recognition site; other site 387092004274 dimerization interface [polypeptide binding]; other site 387092004275 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 387092004276 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 387092004277 Walker A motif; other site 387092004278 ATP binding site [chemical binding]; other site 387092004279 Walker B motif; other site 387092004280 arginine finger; other site 387092004281 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 387092004282 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 387092004283 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 387092004284 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 387092004285 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 387092004286 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 387092004287 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 387092004288 30S subunit binding site; other site 387092004289 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 387092004290 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 387092004291 ssDNA binding site; other site 387092004292 generic binding surface II; other site 387092004293 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 387092004294 ATP binding site [chemical binding]; other site 387092004295 putative Mg++ binding site [ion binding]; other site 387092004296 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 387092004297 nucleotide binding region [chemical binding]; other site 387092004298 ATP-binding site [chemical binding]; other site 387092004299 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 387092004300 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 387092004301 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 387092004302 hypothetical protein; Provisional; Region: PRK08445 387092004303 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 387092004304 FeS/SAM binding site; other site 387092004305 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 387092004306 putative active site [active] 387092004307 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 387092004308 putative RNA binding site [nucleotide binding]; other site 387092004309 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 387092004310 homopentamer interface [polypeptide binding]; other site 387092004311 active site 387092004312 Protein of unknown function DUF86; Region: DUF86; pfam01934 387092004313 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 387092004314 active site 387092004315 NTP binding site [chemical binding]; other site 387092004316 metal binding triad [ion binding]; metal-binding site 387092004317 antibiotic binding site [chemical binding]; other site 387092004318 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 387092004319 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 387092004320 putative active site [active] 387092004321 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 387092004322 EamA-like transporter family; Region: EamA; pfam00892 387092004323 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 387092004324 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 387092004325 Mechanosensitive ion channel; Region: MS_channel; pfam00924 387092004326 GTP-binding protein Der; Reviewed; Region: PRK00093 387092004327 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 387092004328 G1 box; other site 387092004329 GTP/Mg2+ binding site [chemical binding]; other site 387092004330 Switch I region; other site 387092004331 G2 box; other site 387092004332 Switch II region; other site 387092004333 G3 box; other site 387092004334 G4 box; other site 387092004335 G5 box; other site 387092004336 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 387092004337 G1 box; other site 387092004338 GTP/Mg2+ binding site [chemical binding]; other site 387092004339 Switch I region; other site 387092004340 G2 box; other site 387092004341 G3 box; other site 387092004342 Switch II region; other site 387092004343 G4 box; other site 387092004344 G5 box; other site 387092004345 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 387092004346 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 387092004347 active site 387092004348 HIGH motif; other site 387092004349 dimer interface [polypeptide binding]; other site 387092004350 KMSKS motif; other site 387092004351 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 387092004352 active site 387092004353 NTP binding site [chemical binding]; other site 387092004354 metal binding triad [ion binding]; metal-binding site 387092004355 antibiotic binding site [chemical binding]; other site 387092004356 HEPN domain; Region: HEPN; pfam05168 387092004357 PII-like signaling protein [Signal transduction mechanisms]; Region: COG1993 387092004358 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 387092004359 Putative amidoligase enzyme; Region: Amidoligase_2; pfam12224 387092004360 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 387092004361 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 387092004362 catalytic triad [active] 387092004363 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 387092004364 seryl-tRNA synthetase; Provisional; Region: PRK05431 387092004365 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 387092004366 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 387092004367 dimer interface [polypeptide binding]; other site 387092004368 active site 387092004369 motif 1; other site 387092004370 motif 2; other site 387092004371 motif 3; other site 387092004372 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 387092004373 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 387092004374 Substrate binding site; other site 387092004375 Cupin domain; Region: Cupin_2; cl17218 387092004376 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 387092004377 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 387092004378 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 387092004379 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 387092004380 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 387092004381 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387092004382 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 387092004383 NAD(P) binding site [chemical binding]; other site 387092004384 active site 387092004385 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 387092004386 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 387092004387 NADP-binding site; other site 387092004388 homotetramer interface [polypeptide binding]; other site 387092004389 substrate binding site [chemical binding]; other site 387092004390 homodimer interface [polypeptide binding]; other site 387092004391 active site 387092004392 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 387092004393 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 387092004394 metal ion-dependent adhesion site (MIDAS); other site 387092004395 PIN domain; Region: PIN; pfam01850 387092004396 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 387092004397 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 387092004398 Probable gene remnant. Similar to the N-terminal region of Desulfitobacterium hafniense DCB-2 transposase (251 aa) DhafDRAFT_1439. 387092004399 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 387092004400 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 387092004401 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 387092004402 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 387092004403 Domain of unknown function (DUF4214); Region: DUF4214; pfam13946 387092004404 Methyltransferase domain; Region: Methyltransf_23; pfam13489 387092004405 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 387092004406 S-adenosylmethionine binding site [chemical binding]; other site 387092004407 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 387092004408 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 387092004409 Walker A/P-loop; other site 387092004410 ATP binding site [chemical binding]; other site 387092004411 Q-loop/lid; other site 387092004412 ABC transporter signature motif; other site 387092004413 Walker B; other site 387092004414 D-loop; other site 387092004415 H-loop/switch region; other site 387092004416 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 387092004417 putative carbohydrate binding site [chemical binding]; other site 387092004418 Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not...; Region: ZnMc_serralysin_like; cd04277 387092004419 active site 387092004420 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 387092004421 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 387092004422 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 387092004423 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092004424 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 387092004425 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 387092004426 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 387092004427 Walker A/P-loop; other site 387092004428 ATP binding site [chemical binding]; other site 387092004429 Q-loop/lid; other site 387092004430 ABC transporter signature motif; other site 387092004431 Walker B; other site 387092004432 D-loop; other site 387092004433 H-loop/switch region; other site 387092004434 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 387092004435 This family is most closely related to the GT1 family of glycosyltransferases. wbaZ in Salmonella enterica has been shown to possess the mannosyl transferase activity. The members of this family are found in certain bacteria and Archaea; Region: GT1_wbaZ_like; cd03804 387092004436 putative ADP-binding pocket [chemical binding]; other site 387092004437 Undecaprenyl-phosphate galactose phosphotransferase, WbaP; Region: WbaP_sugtrans; TIGR03022 387092004438 Bacterial sugar transferase; Region: Bac_transf; pfam02397 387092004439 2-isopropylmalate synthase; Validated; Region: PRK00915 387092004440 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 387092004441 active site 387092004442 catalytic residues [active] 387092004443 metal binding site [ion binding]; metal-binding site 387092004444 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 387092004445 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 387092004446 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 387092004447 FtsH Extracellular; Region: FtsH_ext; pfam06480 387092004448 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 387092004449 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 387092004450 Walker A motif; other site 387092004451 ATP binding site [chemical binding]; other site 387092004452 Walker B motif; other site 387092004453 arginine finger; other site 387092004454 Peptidase family M41; Region: Peptidase_M41; pfam01434 387092004455 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 387092004456 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 387092004457 S-adenosylmethionine binding site [chemical binding]; other site 387092004458 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 387092004459 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 387092004460 catalytic residues [active] 387092004461 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 387092004462 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 387092004463 putative active site [active] 387092004464 oxyanion strand; other site 387092004465 catalytic triad [active] 387092004466 EAL-domain associated signalling protein domain; Region: YkuI_C; pfam10388 387092004467 Cache domain; Region: Cache_1; pfam02743 387092004468 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 387092004469 active site 387092004470 catalytic site [active] 387092004471 substrate binding site [chemical binding]; other site 387092004472 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 387092004473 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 387092004474 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 387092004475 Sulfatase; Region: Sulfatase; pfam00884 387092004476 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 387092004477 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 387092004478 putative NAD(P) binding site [chemical binding]; other site 387092004479 active site 387092004480 putative substrate binding site [chemical binding]; other site 387092004481 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 387092004482 active site 387092004483 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 387092004484 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 387092004485 Hemerythrin-like domain; Region: Hr-like; cd12108 387092004486 Fe binding site [ion binding]; other site 387092004487 Uncharacterized conserved protein (DUF2249); Region: DUF2249; cl17719 387092004488 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 387092004489 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 387092004490 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 387092004491 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 387092004492 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 387092004493 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092004494 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092004495 ATP binding site [chemical binding]; other site 387092004496 Mg2+ binding site [ion binding]; other site 387092004497 G-X-G motif; other site 387092004498 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092004499 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092004500 active site 387092004501 phosphorylation site [posttranslational modification] 387092004502 intermolecular recognition site; other site 387092004503 dimerization interface [polypeptide binding]; other site 387092004504 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 387092004505 DNA binding site [nucleotide binding] 387092004506 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 387092004507 active site 387092004508 substrate binding pocket [chemical binding]; other site 387092004509 dimer interface [polypeptide binding]; other site 387092004510 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 387092004511 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 387092004512 active site 387092004513 substrate binding site [chemical binding]; other site 387092004514 metal binding site [ion binding]; metal-binding site 387092004515 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 387092004516 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 387092004517 Nitrogen regulatory protein P-II; Region: P-II; smart00938 387092004518 UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: GlnD; COG2844 387092004519 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 387092004520 metal binding triad; other site 387092004521 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 387092004522 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 387092004523 ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; Region: ACT_UUR-ACR-like; cd04873 387092004524 nitrite extrusion protein (nitrite facilitator); Region: 2A0108; TIGR00886 387092004525 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 387092004526 putative substrate translocation pore; other site 387092004527 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 387092004528 active site 387092004529 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 387092004530 Catalytic domain of Protein Kinases; Region: PKc; cd00180 387092004531 active site 387092004532 ATP binding site [chemical binding]; other site 387092004533 substrate binding site [chemical binding]; other site 387092004534 activation loop (A-loop); other site 387092004535 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 387092004536 Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and...; Region: TNFR; cl12111 387092004537 parallel homodimerization interface [polypeptide binding]; other site 387092004538 protein binding site [polypeptide binding]; other site 387092004539 50's loop TNF binding site; other site 387092004540 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 387092004541 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 387092004542 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 387092004543 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 387092004544 [4Fe-4S] binding site [ion binding]; other site 387092004545 molybdopterin cofactor binding site; other site 387092004546 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 387092004547 molybdopterin cofactor binding site; other site 387092004548 ferredoxin-nitrite reductase; Reviewed; Region: nirA; PRK09566 387092004549 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 387092004550 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 387092004551 O-Antigen ligase; Region: Wzy_C; pfam04932 387092004552 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 387092004553 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 387092004554 putative active site [active] 387092004555 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 387092004556 active site 387092004557 catalytic triad [active] 387092004558 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 387092004559 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 387092004560 active site 387092004561 dimer interface [polypeptide binding]; other site 387092004562 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 387092004563 Ligand Binding Site [chemical binding]; other site 387092004564 Molecular Tunnel; other site 387092004565 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 387092004566 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 387092004567 putative ADP-binding pocket [chemical binding]; other site 387092004568 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 387092004569 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 387092004570 putative ADP-binding pocket [chemical binding]; other site 387092004571 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 387092004572 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 387092004573 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 387092004574 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 387092004575 putative acyl-acceptor binding pocket; other site 387092004576 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 387092004577 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 387092004578 putative active site [active] 387092004579 ADP-heptose:LPS heptosyl transferase I; Provisional; Region: PRK10964; cl15782 387092004580 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 387092004581 dimer interface [polypeptide binding]; other site 387092004582 active site 387092004583 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 387092004584 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 387092004585 putative ribose interaction site [chemical binding]; other site 387092004586 putative ADP binding site [chemical binding]; other site 387092004587 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 387092004588 active site 387092004589 nucleotide binding site [chemical binding]; other site 387092004590 HIGH motif; other site 387092004591 KMSKS motif; other site 387092004592 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387092004593 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 387092004594 NAD(P) binding site [chemical binding]; other site 387092004595 active site 387092004596 Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]; Region: HisB; COG0241 387092004597 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 387092004598 active site 387092004599 motif I; other site 387092004600 motif II; other site 387092004601 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 387092004602 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 387092004603 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 387092004604 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 387092004605 metal-binding site [ion binding] 387092004606 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 387092004607 Soluble P-type ATPase [General function prediction only]; Region: COG4087 387092004608 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 387092004609 active site 387092004610 transcription termination factor Rho; Provisional; Region: rho; PRK09376 387092004611 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 387092004612 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 387092004613 RNA binding site [nucleotide binding]; other site 387092004614 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 387092004615 multimer interface [polypeptide binding]; other site 387092004616 Walker A motif; other site 387092004617 ATP binding site [chemical binding]; other site 387092004618 Walker B motif; other site 387092004619 glutamate racemase; Provisional; Region: PRK00865 387092004620 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 387092004621 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 387092004622 Walker A motif; other site 387092004623 ATP binding site [chemical binding]; other site 387092004624 Walker B motif; other site 387092004625 arginine finger; other site 387092004626 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 387092004627 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 387092004628 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 387092004629 minor groove reading motif; other site 387092004630 helix-hairpin-helix signature motif; other site 387092004631 active site 387092004632 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 387092004633 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 387092004634 putative active site [active] 387092004635 metal binding site [ion binding]; metal-binding site 387092004636 homodimer binding site [polypeptide binding]; other site 387092004637 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 387092004638 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 387092004639 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 387092004640 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 387092004641 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 387092004642 ATP binding site [chemical binding]; other site 387092004643 putative Mg++ binding site [ion binding]; other site 387092004644 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 387092004645 nucleotide binding region [chemical binding]; other site 387092004646 ATP-binding site [chemical binding]; other site 387092004647 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 387092004648 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 387092004649 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 387092004650 Lipopolysaccharide-assembly; Region: LptE; pfam04390 387092004651 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 387092004652 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 387092004653 HIGH motif; other site 387092004654 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 387092004655 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 387092004656 active site 387092004657 KMSKS motif; other site 387092004658 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 387092004659 tRNA binding surface [nucleotide binding]; other site 387092004660 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 387092004661 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 387092004662 Protein export membrane protein; Region: SecD_SecF; pfam02355 387092004663 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 387092004664 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 387092004665 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 387092004666 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 387092004667 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 387092004668 active site 387092004669 catalytic triad [active] 387092004670 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 387092004671 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 387092004672 dimer interface [polypeptide binding]; other site 387092004673 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092004674 catalytic residue [active] 387092004675 hypothetical protein; Provisional; Region: PRK07101 387092004676 substrate-cofactor binding pocket; other site 387092004677 Transcriptional regulator [Transcription]; Region: LysR; COG0583 387092004678 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 387092004679 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 387092004680 putative dimerization interface [polypeptide binding]; other site 387092004681 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 387092004682 Part of AAA domain; Region: AAA_19; pfam13245 387092004683 Family description; Region: UvrD_C_2; pfam13538 387092004684 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK04099 387092004685 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 387092004686 RNA binding site [nucleotide binding]; other site 387092004687 active site 387092004688 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 387092004689 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 387092004690 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 387092004691 SmpB-tmRNA interface; other site 387092004692 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092004693 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092004694 metal binding site [ion binding]; metal-binding site 387092004695 active site 387092004696 I-site; other site 387092004697 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 387092004698 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 387092004699 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 387092004700 FeS/SAM binding site; other site 387092004701 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 387092004702 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 387092004703 Ligand Binding Site [chemical binding]; other site 387092004704 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 387092004705 putative acyl-acceptor binding pocket; other site 387092004706 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 387092004707 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 387092004708 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 387092004709 FeS/SAM binding site; other site 387092004710 TRAM domain; Region: TRAM; pfam01938 387092004711 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 387092004712 NusA N-terminal domain; Region: NusA_N; pfam08529 387092004713 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 387092004714 RNA binding site [nucleotide binding]; other site 387092004715 homodimer interface [polypeptide binding]; other site 387092004716 NusA-like KH domain; Region: KH_5; pfam13184 387092004717 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 387092004718 G-X-X-G motif; other site 387092004719 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 387092004720 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 387092004721 dimer interface [polypeptide binding]; other site 387092004722 conserved gate region; other site 387092004723 putative PBP binding loops; other site 387092004724 ABC-ATPase subunit interface; other site 387092004725 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 387092004726 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 387092004727 NAD binding site [chemical binding]; other site 387092004728 homotetramer interface [polypeptide binding]; other site 387092004729 homodimer interface [polypeptide binding]; other site 387092004730 substrate binding site [chemical binding]; other site 387092004731 active site 387092004732 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 387092004733 triosephosphate isomerase; Provisional; Region: PRK14565 387092004734 substrate binding site [chemical binding]; other site 387092004735 dimer interface [polypeptide binding]; other site 387092004736 catalytic triad [active] 387092004737 Phosphoglycerate kinase; Region: PGK; pfam00162 387092004738 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 387092004739 substrate binding site [chemical binding]; other site 387092004740 hinge regions; other site 387092004741 ADP binding site [chemical binding]; other site 387092004742 catalytic site [active] 387092004743 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 387092004744 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 387092004745 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 387092004746 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 387092004747 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 387092004748 active site 387092004749 (T/H)XGH motif; other site 387092004750 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 387092004751 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 387092004752 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 387092004753 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 387092004754 active site 387092004755 HIGH motif; other site 387092004756 KMSK motif region; other site 387092004757 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 387092004758 tRNA binding surface [nucleotide binding]; other site 387092004759 anticodon binding site; other site 387092004760 twin arginine-targeting protein translocase, TatA/E family; Region: tatAE; TIGR01411 387092004761 Guanylate kinase; Region: Guanylate_kin; pfam00625 387092004762 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 387092004763 catalytic site [active] 387092004764 G-X2-G-X-G-K; other site 387092004765 nuclease NucT; Provisional; Region: PRK13912 387092004766 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 387092004767 putative active site [active] 387092004768 catalytic site [active] 387092004769 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 387092004770 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 387092004771 16S rRNA processing protein RimM; Region: 16S_RimM; TIGR02273 387092004772 RimM N-terminal domain; Region: RimM; pfam01782 387092004773 PRC-barrel domain; Region: PRC; pfam05239 387092004774 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 387092004775 KH domain; Region: KH_4; pfam13083 387092004776 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 387092004777 signal recognition particle protein; Provisional; Region: PRK10867 387092004778 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 387092004779 P loop; other site 387092004780 GTP binding site [chemical binding]; other site 387092004781 Signal peptide binding domain; Region: SRP_SPB; pfam02978 387092004782 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 387092004783 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 387092004784 RNA binding surface [nucleotide binding]; other site 387092004785 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 387092004786 active site 387092004787 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 387092004788 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 387092004789 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 387092004790 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 387092004791 Putative zinc ribbon domain; Region: DUF164; pfam02591 387092004792 Uncharacterized conserved protein [Function unknown]; Region: COG0327 387092004793 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 387092004794 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 387092004795 dimer interface [polypeptide binding]; other site 387092004796 motif 1; other site 387092004797 active site 387092004798 motif 2; other site 387092004799 motif 3; other site 387092004800 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 387092004801 catalytic residues [active] 387092004802 Protein of unknown function DUF89; Region: DUF89; cl15397 387092004803 AIR carboxylase; Region: AIRC; smart01001 387092004804 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 387092004805 Peptidase family U32; Region: Peptidase_U32; pfam01136 387092004806 metal binding site [ion binding]; metal-binding site 387092004807 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 387092004808 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 387092004809 histidinol-phosphatase; Provisional; Region: PRK07328 387092004810 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Region: PHP_HisPPase_Hisj_like; cd12110 387092004811 active site 387092004812 dimer interface [polypeptide binding]; other site 387092004813 glutamine synthetase, type I; Region: GlnA; TIGR00653 387092004814 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 387092004815 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 387092004816 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 387092004817 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 387092004818 TrkA-N domain; Region: TrkA_N; pfam02254 387092004819 Transglycosylase; Region: Transgly; pfam00912 387092004820 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 387092004821 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 387092004822 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 387092004823 Walker A/P-loop; other site 387092004824 ATP binding site [chemical binding]; other site 387092004825 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 387092004826 Q-loop/lid; other site 387092004827 ABC transporter signature motif; other site 387092004828 Walker B; other site 387092004829 D-loop; other site 387092004830 H-loop/switch region; other site 387092004831 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 387092004832 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 387092004833 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 387092004834 catalytic residue [active] 387092004835 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 387092004836 active site 387092004837 substrate binding site [chemical binding]; other site 387092004838 ATP binding site [chemical binding]; other site 387092004839 Maf-like protein; Region: Maf; pfam02545 387092004840 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 387092004841 active site 387092004842 dimer interface [polypeptide binding]; other site 387092004843 S-adenosylmethionine decarboxylase proenzyme; Provisional; Region: PRK03124 387092004844 Predicted integral membrane protein [Function unknown]; Region: COG5615 387092004845 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 387092004846 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 387092004847 motif 1; other site 387092004848 active site 387092004849 motif 2; other site 387092004850 motif 3; other site 387092004851 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 387092004852 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 387092004853 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 387092004854 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 387092004855 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 387092004856 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 387092004857 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 387092004858 active site 387092004859 homodimer interface [polypeptide binding]; other site 387092004860 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092004861 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092004862 metal binding site [ion binding]; metal-binding site 387092004863 active site 387092004864 I-site; other site 387092004865 pantoate--beta-alanine ligase; Region: panC; TIGR00018 387092004866 Pantoate-beta-alanine ligase; Region: PanC; cd00560 387092004867 active site 387092004868 ATP-binding site [chemical binding]; other site 387092004869 pantoate-binding site; other site 387092004870 HXXH motif; other site 387092004871 peptide chain release factor 2; Validated; Region: prfB; PRK00578 387092004872 This domain is found in peptide chain release factors; Region: PCRF; smart00937 387092004873 RF-1 domain; Region: RF-1; pfam00472 387092004874 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 387092004875 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 387092004876 Walker A/P-loop; other site 387092004877 ATP binding site [chemical binding]; other site 387092004878 Q-loop/lid; other site 387092004879 ABC transporter signature motif; other site 387092004880 Walker B; other site 387092004881 D-loop; other site 387092004882 H-loop/switch region; other site 387092004883 elongation factor Ts; Provisional; Region: tsf; PRK09377 387092004884 UBA/TS-N domain; Region: UBA; pfam00627 387092004885 Elongation factor TS; Region: EF_TS; pfam00889 387092004886 Elongation factor TS; Region: EF_TS; pfam00889 387092004887 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 387092004888 rRNA interaction site [nucleotide binding]; other site 387092004889 S8 interaction site; other site 387092004890 putative laminin-1 binding site; other site 387092004891 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 387092004892 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 387092004893 catalytic triad [active] 387092004894 Protein of unknown function (DUF523); Region: DUF523; pfam04463 387092004895 response regulator PleD; Reviewed; Region: pleD; PRK09581 387092004896 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092004897 active site 387092004898 phosphorylation site [posttranslational modification] 387092004899 intermolecular recognition site; other site 387092004900 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092004901 active site 387092004902 phosphorylation site [posttranslational modification] 387092004903 intermolecular recognition site; other site 387092004904 dimerization interface [polypeptide binding]; other site 387092004905 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092004906 metal binding site [ion binding]; metal-binding site 387092004907 active site 387092004908 I-site; other site 387092004909 Uncharacterized ALDH (y4uC) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1; Region: ALDH_y4uC; cd07149 387092004910 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 387092004911 NAD(P) binding site [chemical binding]; other site 387092004912 catalytic residues [active] 387092004913 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 387092004914 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 387092004915 homodimer interface [polypeptide binding]; other site 387092004916 substrate-cofactor binding pocket; other site 387092004917 catalytic residue [active] 387092004918 SPFH domain / Band 7 family; Region: Band_7; pfam01145 387092004919 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 387092004920 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 387092004921 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 387092004922 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 387092004923 metal binding site [ion binding]; metal-binding site 387092004924 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2; cl00208 387092004925 CAS motifs; other site 387092004926 active site 387092004927 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 387092004928 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 387092004929 amidophosphoribosyltransferase; Provisional; Region: PRK08525 387092004930 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 387092004931 active site 387092004932 tetramer interface [polypeptide binding]; other site 387092004933 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 387092004934 active site 387092004935 dihydrodipicolinate reductase; Provisional; Region: PRK00048 387092004936 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 387092004937 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 387092004938 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 387092004939 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 387092004940 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 387092004941 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 387092004942 catalytic residues [active] 387092004943 hypothetical protein; Reviewed; Region: PRK12497 387092004944 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 387092004945 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 387092004946 molybdopterin cofactor binding site; other site 387092004947 Molydopterin dinucleotide binding domain; Region: Molydop_binding; pfam01568 387092004948 molybdopterin cofactor binding site; other site 387092004949 homoserine dehydrogenase; Provisional; Region: PRK06349 387092004950 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 387092004951 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 387092004952 aspartate aminotransferase; Provisional; Region: PRK08636 387092004953 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 387092004954 pyridoxal 5'-phosphate binding site [chemical binding]; other site 387092004955 homodimer interface [polypeptide binding]; other site 387092004956 catalytic residue [active] 387092004957 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 387092004958 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 387092004959 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 387092004960 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 387092004961 Predicted methyltransferases [General function prediction only]; Region: COG0313 387092004962 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 387092004963 putative SAM binding site [chemical binding]; other site 387092004964 putative homodimer interface [polypeptide binding]; other site 387092004965 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 387092004966 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 387092004967 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 387092004968 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 387092004969 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 387092004970 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 387092004971 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 387092004972 Walker A motif; other site 387092004973 ATP binding site [chemical binding]; other site 387092004974 Walker B motif; other site 387092004975 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 387092004976 binding surface 387092004977 TPR motif; other site 387092004978 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 387092004979 AAA domain; Region: AAA_22; pfam13401 387092004980 Walker A motif; other site 387092004981 ATP binding site [chemical binding]; other site 387092004982 Walker B motif; other site 387092004983 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 387092004984 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 387092004985 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 387092004986 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 387092004987 RNA methyltransferase, RsmE family; Region: TIGR00046 387092004988 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 387092004989 Uncharacterized conserved protein [Function unknown]; Region: COG2445 387092004990 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 387092004991 active site 387092004992 NTP binding site [chemical binding]; other site 387092004993 metal binding triad [ion binding]; metal-binding site 387092004994 antibiotic binding site [chemical binding]; other site 387092004995 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 387092004996 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 387092004997 dimer interface [polypeptide binding]; other site 387092004998 putative functional site; other site 387092004999 putative MPT binding site; other site 387092005000 Cytochrome c; Region: Cytochrom_C; cl11414 387092005001 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 387092005002 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 387092005003 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 387092005004 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 387092005005 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 387092005006 FeS/SAM binding site; other site 387092005007 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 387092005008 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 387092005009 Cytochrome c; Region: Cytochrom_C; pfam00034 387092005010 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 387092005011 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 387092005012 intrachain domain interface; other site 387092005013 interchain domain interface [polypeptide binding]; other site 387092005014 heme bH binding site [chemical binding]; other site 387092005015 Qi binding site; other site 387092005016 heme bL binding site [chemical binding]; other site 387092005017 Qo binding site; other site 387092005018 interchain domain interface [polypeptide binding]; other site 387092005019 intrachain domain interface; other site 387092005020 Qi binding site; other site 387092005021 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 387092005022 Qo binding site; other site 387092005023 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 387092005024 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 387092005025 [2Fe-2S] cluster binding site [ion binding]; other site 387092005026 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 387092005027 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 387092005028 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 387092005029 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 387092005030 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 387092005031 Lumazine binding domain; Region: Lum_binding; pfam00677 387092005032 Lumazine binding domain; Region: Lum_binding; pfam00677 387092005033 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; pfam10087 387092005034 Pseudogene. Similar to conserved hypothetical protein. This CDS appears to have a frameshift mutation following codon 58. 387092005035 Probable gene remnant. Similar to the N-terminal region of Thiomicrospira denitrificans ATCC 33889 hypothetical protein (315 aa) Tmden_1345. 387092005036 Probable gene remnant. Similar to the C-terminal region of Thiomicrospira denitrificans ATCC 33889 hypothetical protein (315 aa) Tmden_1345. 387092005037 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 387092005038 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 387092005039 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 387092005040 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 387092005041 dimer interface [polypeptide binding]; other site 387092005042 conserved gate region; other site 387092005043 putative PBP binding loops; other site 387092005044 ABC-ATPase subunit interface; other site 387092005045 ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG4525 387092005046 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 387092005047 Walker A/P-loop; other site 387092005048 ATP binding site [chemical binding]; other site 387092005049 Q-loop/lid; other site 387092005050 ABC transporter signature motif; other site 387092005051 Walker B; other site 387092005052 D-loop; other site 387092005053 H-loop/switch region; other site 387092005054 NnrS protein; Region: NnrS; pfam05940 387092005055 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 387092005056 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 387092005057 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 387092005058 Cupin domain; Region: Cupin_2; pfam07883 387092005059 AmmeMemoRadiSam system protein A; Region: AmmeMemoSam_A; TIGR04335 387092005060 AMMECR1; Region: AMMECR1; pfam01871 387092005061 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092005062 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092005063 metal binding site [ion binding]; metal-binding site 387092005064 active site 387092005065 I-site; other site 387092005066 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 387092005067 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 387092005068 S-ribosylhomocysteinase; Provisional; Region: PRK02260 387092005069 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 387092005070 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 387092005071 TPP-binding site [chemical binding]; other site 387092005072 putative dimer interface [polypeptide binding]; other site 387092005073 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 387092005074 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 387092005075 dimer interface [polypeptide binding]; other site 387092005076 PYR/PP interface [polypeptide binding]; other site 387092005077 TPP binding site [chemical binding]; other site 387092005078 substrate binding site [chemical binding]; other site 387092005079 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 387092005080 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 387092005081 4Fe-4S binding domain; Region: Fer4; pfam00037 387092005082 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 387092005083 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 387092005084 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 387092005085 Eukaryotic phosphomannomutase; Region: PMM; cl17107 387092005086 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 387092005087 motif II; other site 387092005088 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 387092005089 The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold; Region: PBP2_AppA_like; cd08514 387092005090 peptide binding site [polypeptide binding]; other site 387092005091 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 387092005092 active site residue [active] 387092005093 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 387092005094 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 387092005095 23S rRNA interface [nucleotide binding]; other site 387092005096 L3 interface [polypeptide binding]; other site 387092005097 FixH; Region: FixH; pfam05751 387092005098 YtkA-like; Region: YtkA; pfam13115 387092005099 Repair protein; Region: Repair_PSII; cl01535 387092005100 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 387092005101 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 387092005102 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 387092005103 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 387092005104 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 387092005105 Cytochrome c; Region: Cytochrom_C; pfam00034 387092005106 Cytochrome c; Region: Cytochrom_C; pfam00034 387092005107 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 387092005108 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 387092005109 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 387092005110 cbb3-type cytochrome c oxidase subunit I; Provisional; Region: PRK14488 387092005111 Low-spin heme binding site [chemical binding]; other site 387092005112 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 387092005113 D-pathway; other site 387092005114 Putative water exit pathway; other site 387092005115 Binuclear center (active site) [active] 387092005116 K-pathway; other site 387092005117 Putative proton exit pathway; other site 387092005118 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 387092005119 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092005120 active site 387092005121 phosphorylation site [posttranslational modification] 387092005122 intermolecular recognition site; other site 387092005123 dimerization interface [polypeptide binding]; other site 387092005124 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 387092005125 DNA binding site [nucleotide binding] 387092005126 PAS domain; Region: PAS_9; pfam13426 387092005127 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092005128 putative active site [active] 387092005129 heme pocket [chemical binding]; other site 387092005130 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092005131 ATP binding site [chemical binding]; other site 387092005132 Mg2+ binding site [ion binding]; other site 387092005133 G-X-G motif; other site 387092005134 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 387092005135 N-terminal plug; other site 387092005136 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 387092005137 ligand-binding site [chemical binding]; other site 387092005138 proline/glycine betaine transporter; Provisional; Region: PRK10642 387092005139 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 387092005140 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 387092005141 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 387092005142 catalytic site [active] 387092005143 subunit interface [polypeptide binding]; other site 387092005144 Protein of unknown function (DUF507); Region: DUF507; pfam04368 387092005145 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 387092005146 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 387092005147 GDP-binding site [chemical binding]; other site 387092005148 ACT binding site; other site 387092005149 IMP binding site; other site 387092005150 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12293 387092005151 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 387092005152 motif 1; other site 387092005153 dimer interface [polypeptide binding]; other site 387092005154 active site 387092005155 motif 2; other site 387092005156 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 387092005157 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 387092005158 catalytic residue [active] 387092005159 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 387092005160 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 387092005161 putative dimer interface [polypeptide binding]; other site 387092005162 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 387092005163 active site 387092005164 dimerization interface [polypeptide binding]; other site 387092005165 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 387092005166 Major Facilitator Superfamily; Region: MFS_1; pfam07690 387092005167 putative substrate translocation pore; other site 387092005168 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 387092005169 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 387092005170 catalytic residues [active] 387092005171 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 387092005172 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 387092005173 dimer interface [polypeptide binding]; other site 387092005174 putative functional site; other site 387092005175 putative MPT binding site; other site 387092005176 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 387092005177 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 387092005178 MoaE homodimer interface [polypeptide binding]; other site 387092005179 MoaD interaction [polypeptide binding]; other site 387092005180 active site residues [active] 387092005181 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 387092005182 thiS-thiF/thiG interaction site; other site 387092005183 Menaquinone biosynthesis; Region: VitK2_biosynth; pfam02621 387092005184 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 387092005185 hypothetical protein; Reviewed; Region: PRK09790 387092005186 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092005187 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092005188 metal binding site [ion binding]; metal-binding site 387092005189 active site 387092005190 I-site; other site 387092005191 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 387092005192 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 387092005193 Malic enzyme, N-terminal domain; Region: malic; pfam00390 387092005194 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 387092005195 putative NAD(P) binding site [chemical binding]; other site 387092005196 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 387092005197 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 387092005198 active site 387092005199 HIGH motif; other site 387092005200 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 387092005201 active site 387092005202 KMSKS motif; other site 387092005203 SurA N-terminal domain; Region: SurA_N; pfam09312 387092005204 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 387092005205 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 387092005206 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 387092005207 putative trimer interface [polypeptide binding]; other site 387092005208 putative CoA binding site [chemical binding]; other site 387092005209 biotin carboxylase; Validated; Region: PRK08462 387092005210 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 387092005211 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 387092005212 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 387092005213 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 387092005214 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 387092005215 carboxyltransferase (CT) interaction site; other site 387092005216 biotinylation site [posttranslational modification]; other site 387092005217 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 387092005218 trimer interface [polypeptide binding]; other site 387092005219 active site 387092005220 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092005221 metal binding site [ion binding]; metal-binding site 387092005222 active site 387092005223 I-site; other site 387092005224 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 387092005225 Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]; Region: AsnB; COG0367 387092005226 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 387092005227 active site 387092005228 dimer interface [polypeptide binding]; other site 387092005229 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 387092005230 Ligand Binding Site [chemical binding]; other site 387092005231 Molecular Tunnel; other site 387092005232 Thermotoga maritima CorA-like family; Region: TmCorA-like; cd12822 387092005233 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 387092005234 oligomer interface [polypeptide binding]; other site 387092005235 metal binding site [ion binding]; metal-binding site 387092005236 metal binding site [ion binding]; metal-binding site 387092005237 putative Cl binding site [ion binding]; other site 387092005238 aspartate ring; other site 387092005239 basic sphincter; other site 387092005240 hydrophobic gate; other site 387092005241 periplasmic entrance; other site 387092005242 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 387092005243 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 387092005244 DNA topoisomerase I; Validated; Region: PRK05582 387092005245 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 387092005246 active site 387092005247 interdomain interaction site; other site 387092005248 putative metal-binding site [ion binding]; other site 387092005249 nucleotide binding site [chemical binding]; other site 387092005250 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 387092005251 domain I; other site 387092005252 DNA binding groove [nucleotide binding] 387092005253 phosphate binding site [ion binding]; other site 387092005254 domain II; other site 387092005255 domain III; other site 387092005256 nucleotide binding site [chemical binding]; other site 387092005257 catalytic site [active] 387092005258 domain IV; other site 387092005259 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 387092005260 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 387092005261 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 387092005262 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 387092005263 active site 387092005264 metal binding site [ion binding]; metal-binding site 387092005265 homotetramer interface [polypeptide binding]; other site 387092005266 biotin synthase; Provisional; Region: PRK08508 387092005267 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 387092005268 FeS/SAM binding site; other site 387092005269 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 387092005270 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 387092005271 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 387092005272 AMIN domain; Region: AMIN; pfam11741 387092005273 enolase; Provisional; Region: eno; PRK00077 387092005274 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 387092005275 dimer interface [polypeptide binding]; other site 387092005276 metal binding site [ion binding]; metal-binding site 387092005277 substrate binding pocket [chemical binding]; other site 387092005278 recombinase A; Provisional; Region: recA; PRK09354 387092005279 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 387092005280 hexamer interface [polypeptide binding]; other site 387092005281 Walker A motif; other site 387092005282 ATP binding site [chemical binding]; other site 387092005283 Walker B motif; other site 387092005284 Menaquinone biosynthesis; Region: VitK2_biosynth; cl17475 387092005285 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092005286 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092005287 metal binding site [ion binding]; metal-binding site 387092005288 active site 387092005289 I-site; other site 387092005290 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 387092005291 FAD binding domain; Region: FAD_binding_4; pfam01565 387092005292 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 387092005293 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 387092005294 dimer interface [polypeptide binding]; other site 387092005295 catalytic triad [active] 387092005296 peroxidatic and resolving cysteines [active] 387092005297 UGMP family protein; Validated; Region: PRK09604 387092005298 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 387092005299 Serine hydrolase; Region: Ser_hydrolase; cl17834 387092005300 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 387092005301 major vault protein; Provisional; Region: PTZ00491 387092005302 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 387092005303 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 387092005304 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 387092005305 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 387092005306 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 387092005307 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 387092005308 Domain of unknown function (DUF814); Region: DUF814; pfam05670 387092005309 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 387092005310 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 387092005311 substrate binding site [chemical binding]; other site 387092005312 ligand binding site [chemical binding]; other site 387092005313 Sugar fermentation stimulation protein; Region: SfsA; cl00647 387092005314 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 387092005315 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 387092005316 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092005317 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 387092005318 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 387092005319 Walker A/P-loop; other site 387092005320 ATP binding site [chemical binding]; other site 387092005321 Q-loop/lid; other site 387092005322 ABC transporter signature motif; other site 387092005323 Walker B; other site 387092005324 D-loop; other site 387092005325 H-loop/switch region; other site 387092005326 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 387092005327 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 387092005328 FtsX-like permease family; Region: FtsX; pfam02687 387092005329 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 387092005330 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 387092005331 FtsX-like permease family; Region: FtsX; pfam02687 387092005332 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_a; cd09179 387092005333 putative active site [active] 387092005334 catalytic site [active] 387092005335 DNA phosphorothioation system restriction enzyme; Region: dnd_restrict_1; TIGR04095 387092005336 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 387092005337 ATP binding site [chemical binding]; other site 387092005338 putative Mg++ binding site [ion binding]; other site 387092005339 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 387092005340 nucleotide binding region [chemical binding]; other site 387092005341 ATP-binding site [chemical binding]; other site 387092005342 DNA sulfur modification protein DndD; Region: DNA_S_dndD; TIGR03185 387092005343 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092005344 Walker A/P-loop; other site 387092005345 ATP binding site [chemical binding]; other site 387092005346 Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; Region: SPEC; cl02488 387092005347 linker region; other site 387092005348 dnd system-associated protein 4; Region: dnd_assoc_4; TIGR04062 387092005349 Uncharacterized conserved protein [Function unknown]; Region: COG1479 387092005350 Protein of unknown function DUF262; Region: DUF262; pfam03235 387092005351 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 387092005352 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 387092005353 AAA domain; Region: AAA_23; pfam13476 387092005354 Walker A/P-loop; other site 387092005355 ATP binding site [chemical binding]; other site 387092005356 putative sulfurtransferase DndC; Region: DNA_S_dndC; TIGR03183 387092005357 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 387092005358 Active Sites [active] 387092005359 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 387092005360 non-specific DNA binding site [nucleotide binding]; other site 387092005361 salt bridge; other site 387092005362 sequence-specific DNA binding site [nucleotide binding]; other site 387092005363 Carbohydrate phosphorylase; Region: Phosphorylase; pfam00343 387092005364 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 387092005365 Walker A motif; other site 387092005366 ATP binding site [chemical binding]; other site 387092005367 Walker B motif; other site 387092005368 TrwC relaxase; Region: TrwC; pfam08751 387092005369 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 387092005370 AAA domain; Region: AAA_30; pfam13604 387092005371 Family description; Region: UvrD_C_2; pfam13538 387092005372 Helix-turn-helix domain; Region: HTH_17; cl17695 387092005373 integrase; Provisional; Region: int; PHA02601 387092005374 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 387092005375 active site 387092005376 catalytic residues [active] 387092005377 DNA binding site [nucleotide binding] 387092005378 Int/Topo IB signature motif; other site 387092005379 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 387092005380 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG5633 387092005381 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 387092005382 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 387092005383 putative dimer interface [polypeptide binding]; other site 387092005384 Protein of unknown function (DUF3897); Region: DUF3897; pfam13036 387092005385 LPP20 lipoprotein; Region: LPP20; cl15824 387092005386 Curli production assembly/transport component CsgG; Region: CsgG; cl17434 387092005387 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 387092005388 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 387092005389 GTP binding site; other site 387092005390 Stress responsive A/B Barrel Domain; Region: Dabb; smart00886 387092005391 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 387092005392 trimer interface [polypeptide binding]; other site 387092005393 dimer interface [polypeptide binding]; other site 387092005394 putative active site [active] 387092005395 Protein of unknown function (DUF541); Region: SIMPL; cl01077 387092005396 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 387092005397 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 387092005398 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 387092005399 ATP binding site [chemical binding]; other site 387092005400 putative Mg++ binding site [ion binding]; other site 387092005401 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 387092005402 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 387092005403 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 387092005404 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 387092005405 Divergent AAA domain; Region: AAA_4; pfam04326 387092005406 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 387092005407 active site 2 [active] 387092005408 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 387092005409 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 387092005410 Fic/DOC family; Region: Fic; pfam02661 387092005411 HsdM N-terminal domain; Region: HsdM_N; pfam12161 387092005412 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 387092005413 Methyltransferase domain; Region: Methyltransf_26; pfam13659 387092005414 hypothetical protein; Reviewed; Region: PRK00024 387092005415 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 387092005416 MPN+ (JAMM) motif; other site 387092005417 Zinc-binding site [ion binding]; other site 387092005418 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 387092005419 DEAD-like helicases superfamily; Region: DEXDc; smart00487 387092005420 ATP binding site [chemical binding]; other site 387092005421 Mg++ binding site [ion binding]; other site 387092005422 motif III; other site 387092005423 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 387092005424 nucleotide binding region [chemical binding]; other site 387092005425 ATP-binding site [chemical binding]; other site 387092005426 BON domain; Region: BON; pfam04972 387092005427 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 387092005428 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 387092005429 active site 387092005430 dimerization interface [polypeptide binding]; other site 387092005431 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 387092005432 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 387092005433 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 387092005434 protein binding site [polypeptide binding]; other site 387092005435 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 387092005436 protein binding site [polypeptide binding]; other site 387092005437 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092005438 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092005439 active site 387092005440 phosphorylation site [posttranslational modification] 387092005441 intermolecular recognition site; other site 387092005442 dimerization interface [polypeptide binding]; other site 387092005443 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 387092005444 DNA binding site [nucleotide binding] 387092005445 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092005446 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 387092005447 dimerization interface [polypeptide binding]; other site 387092005448 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 387092005449 dimer interface [polypeptide binding]; other site 387092005450 phosphorylation site [posttranslational modification] 387092005451 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092005452 ATP binding site [chemical binding]; other site 387092005453 Mg2+ binding site [ion binding]; other site 387092005454 G-X-G motif; other site 387092005455 Ion channel; Region: Ion_trans_2; pfam07885 387092005456 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 387092005457 TrkA-N domain; Region: TrkA_N; pfam02254 387092005458 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 387092005459 TrkA-N domain; Region: TrkA_N; pfam02254 387092005460 hypothetical protein; Provisional; Region: PRK10279 387092005461 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 387092005462 active site 387092005463 nucleophile elbow; other site 387092005464 Outer membrane efflux protein; Region: OEP; pfam02321 387092005465 Outer membrane efflux protein; Region: OEP; pfam02321 387092005466 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 387092005467 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 387092005468 putative substrate translocation pore; other site 387092005469 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 387092005470 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092005471 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 387092005472 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 387092005473 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 387092005474 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 387092005475 HlyD family secretion protein; Region: HlyD_3; pfam13437 387092005476 Major Facilitator Superfamily; Region: MFS_1; pfam07690 387092005477 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 387092005478 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 387092005479 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 387092005480 Walker A/P-loop; other site 387092005481 ATP binding site [chemical binding]; other site 387092005482 Q-loop/lid; other site 387092005483 ABC transporter signature motif; other site 387092005484 Walker B; other site 387092005485 D-loop; other site 387092005486 H-loop/switch region; other site 387092005487 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 387092005488 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 387092005489 Walker A/P-loop; other site 387092005490 ATP binding site [chemical binding]; other site 387092005491 Q-loop/lid; other site 387092005492 ABC transporter signature motif; other site 387092005493 Walker B; other site 387092005494 D-loop; other site 387092005495 H-loop/switch region; other site 387092005496 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 387092005497 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 387092005498 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 387092005499 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 387092005500 Protein of unknown function (DUF3187); Region: DUF3187; pfam11383 387092005501 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 387092005502 dinuclear metal binding motif [ion binding]; other site 387092005503 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 387092005504 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 387092005505 Mechanosensitive ion channel; Region: MS_channel; pfam00924 387092005506 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092005507 metal binding site [ion binding]; metal-binding site 387092005508 active site 387092005509 I-site; other site 387092005510 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 387092005511 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 387092005512 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 387092005513 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 387092005514 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 387092005515 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 387092005516 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 387092005517 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 387092005518 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 387092005519 Bacterial transcriptional repressor; Region: TetR; pfam13972 387092005520 Pseudogene. Similar to signal transduction response regulator, GGDEF family protein. This CDS appears to have a frameshift mutation following codon 445. 387092005521 Probable gene remnant. Similar to the C-terminal region of Clostridium beijerincki NCIMB 8052 signal transduction response regulator, GGDEF family protein (821 aa) CbeiDRAFT_0509. 387092005522 Probable gene remnant. Similar to the N-terminal region of Clostridium beijerincki NCIMB 8052 signal transduction response regulator, GGDEF family protein (821 aa) CbeiDRAFT_0509. 387092005523 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 387092005524 TrkA-N domain; Region: TrkA_N; pfam02254 387092005525 TrkA-C domain; Region: TrkA_C; pfam02080 387092005526 TrkA-N domain; Region: TrkA_N; pfam02254 387092005527 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 387092005528 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 387092005529 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 387092005530 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 387092005531 Cl- selectivity filter; other site 387092005532 Cl- binding residues [ion binding]; other site 387092005533 pore gating glutamate residue; other site 387092005534 dimer interface [polypeptide binding]; other site 387092005535 Family description; Region: DsbD_2; pfam13386 387092005536 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 387092005537 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 387092005538 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 387092005539 Flavin reductase like domain; Region: Flavin_Reduct; pfam01613 387092005540 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 387092005541 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 387092005542 FeS/SAM binding site; other site 387092005543 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 387092005544 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 387092005545 FeS/SAM binding site; other site 387092005546 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 387092005547 Na/Pi-cotransporter; Region: NaPi_cotrn_rel; TIGR00704 387092005548 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 387092005549 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 387092005550 putative amphipathic alpha helix; other site 387092005551 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092005552 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 387092005553 dimer interface [polypeptide binding]; other site 387092005554 phosphorylation site [posttranslational modification] 387092005555 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092005556 ATP binding site [chemical binding]; other site 387092005557 Mg2+ binding site [ion binding]; other site 387092005558 G-X-G motif; other site 387092005559 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092005560 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092005561 intermolecular recognition site; other site 387092005562 active site 387092005563 dimerization interface [polypeptide binding]; other site 387092005564 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 387092005565 DNA binding site [nucleotide binding] 387092005566 Haem-binding domain; Region: Haem_bd; pfam14376 387092005567 short chain dehydrogenase; Provisional; Region: PRK06924 387092005568 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 387092005569 NAD(P) binding site [chemical binding]; other site 387092005570 active site 387092005571 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 387092005572 ABC transporter periplasmic binding protein, urea carboxylase region; Region: ABC_peri_uca; TIGR03427 387092005573 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092005574 PAS domain; Region: PAS_9; pfam13426 387092005575 putative active site [active] 387092005576 heme pocket [chemical binding]; other site 387092005577 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 387092005578 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 387092005579 metal binding site [ion binding]; metal-binding site 387092005580 active site 387092005581 I-site; other site 387092005582 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 387092005583 reverse gyrase; Reviewed; Region: PRK09401 387092005584 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 387092005585 ATP binding site [chemical binding]; other site 387092005586 putative Mg++ binding site [ion binding]; other site 387092005587 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 387092005588 active site 387092005589 metal binding site [ion binding]; metal-binding site 387092005590 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 387092005591 domain I; other site 387092005592 DNA binding groove [nucleotide binding] 387092005593 phosphate binding site [ion binding]; other site 387092005594 domain II; other site 387092005595 domain III; other site 387092005596 nucleotide binding site [chemical binding]; other site 387092005597 catalytic site [active] 387092005598 domain IV; other site 387092005599 Predicted transcriptional regulators [Transcription]; Region: COG1318 387092005600 probable regulatory domain; Region: near_KaiC_dom; TIGR03879 387092005601 KaiC domain protein, AF_0795 family; Region: thermo_KaiC_2; TIGR03878 387092005602 KaiC; Region: KaiC; pfam06745 387092005603 ATP binding site [chemical binding]; other site 387092005604 Walker A motif; other site 387092005605 Walker B motif; other site 387092005606 PemK-like protein; Region: PemK; pfam02452 387092005607 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 387092005608 active site 387092005609 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 387092005610 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 387092005611 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 387092005612 Sel1-like repeats; Region: SEL1; smart00671 387092005613 Sel1-like repeats; Region: SEL1; smart00671 387092005614 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 387092005615 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 387092005616 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 387092005617 Coenzyme A binding pocket [chemical binding]; other site 387092005618 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 387092005619 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 387092005620 metal binding site [ion binding]; metal-binding site 387092005621 dimer interface [polypeptide binding]; other site 387092005622 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 387092005623 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 387092005624 FeS/SAM binding site; other site 387092005625 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 387092005626 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 387092005627 ATP cone domain; Region: ATP-cone; pfam03477 387092005628 Class III ribonucleotide reductase; Region: RNR_III; cd01675 387092005629 effector binding site; other site 387092005630 active site 387092005631 Zn binding site [ion binding]; other site 387092005632 5-oxoprolinase; Region: PLN02666 387092005633 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 387092005634 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 387092005635 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 387092005636 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 387092005637 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 387092005638 domain interfaces; other site 387092005639 active site 387092005640 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 387092005641 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 387092005642 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 387092005643 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 387092005644 NosL; Region: NosL; cl01769 387092005645 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 387092005646 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 387092005647 NosL; Region: NosL; cl01769 387092005648 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 387092005649 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 387092005650 Walker A/P-loop; other site 387092005651 ATP binding site [chemical binding]; other site 387092005652 Q-loop/lid; other site 387092005653 ABC transporter signature motif; other site 387092005654 Walker B; other site 387092005655 D-loop; other site 387092005656 H-loop/switch region; other site 387092005657 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 387092005658 4Fe-4S binding domain; Region: Fer4_5; pfam12801 387092005659 4Fe-4S binding domain; Region: Fer4_6; pfam12837 387092005660 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 387092005661 Cytochrome c; Region: Cytochrom_C; cl11414 387092005662 Cytochrome c; Region: Cytochrom_C; cl11414 387092005663 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 387092005664 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 387092005665 4Fe-4S binding domain; Region: Fer4; pfam00037 387092005666 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 387092005667 nitrous-oxide reductase, Sec-dependent; Region: nitrous_NosZ_Gp; TIGR04246 387092005668 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 387092005669 Cytochrome c; Region: Cytochrom_C; pfam00034 387092005670 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 387092005671 Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis]; Region: DPH5; COG1798 387092005672 active site 387092005673 SAM binding site [chemical binding]; other site 387092005674 homodimer interface [polypeptide binding]; other site 387092005675 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 387092005676 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 387092005677 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 387092005678 FeS/SAM binding site; other site 387092005679 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 387092005680 Cytochrome c; Region: Cytochrom_C; pfam00034 387092005681 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 387092005682 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 387092005683 Cytochrome c; Region: Cytochrom_C; pfam00034 387092005684 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 387092005685 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 387092005686 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 387092005687 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 387092005688 Low-spin heme binding site [chemical binding]; other site 387092005689 D-pathway; other site 387092005690 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 387092005691 Putative water exit pathway; other site 387092005692 K-pathway; other site 387092005693 Binuclear center (active site) [active] 387092005694 Putative proton exit pathway; other site 387092005695 Cytochrome c; Region: Cytochrom_C; pfam00034 387092005696 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 387092005697 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 387092005698 ligand binding site [chemical binding]; other site 387092005699 flexible hinge region; other site 387092005700 helix_turn_helix, cAMP Regulatory protein; Region: HTH_CRP; smart00419 387092005701 non-specific DNA interactions [nucleotide binding]; other site 387092005702 DNA binding site [nucleotide binding] 387092005703 sequence specific DNA binding site [nucleotide binding]; other site 387092005704 putative cAMP binding site [chemical binding]; other site 387092005705 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 387092005706 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 387092005707 PAS fold; Region: PAS_3; pfam08447 387092005708 putative active site [active] 387092005709 heme pocket [chemical binding]; other site 387092005710 NapD protein; Region: NapD; pfam03927 387092005711 FOG: WD40 repeat [General function prediction only]; Region: COG2319 387092005712 FOG: WD40 repeat [General function prediction only]; Region: COG2319 387092005713 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 387092005714 ferredoxin-type protein; Provisional; Region: PRK10194 387092005715 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 387092005716 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 387092005717 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 387092005718 4Fe-4S binding domain; Region: Fer4_5; pfam12801 387092005719 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 387092005720 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 387092005721 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 387092005722 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 387092005723 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 387092005724 molybdopterin cofactor binding site; other site 387092005725 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 387092005726 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 387092005727 molybdopterin cofactor binding site; other site 387092005728 Domain of unknown function (DUF1858); Region: DUF1858; pfam08984 387092005729 Uncharacterized conserved protein (DUF2249); Region: DUF2249; cl17719 387092005730 Domain of unknown function DUF59; Region: DUF59; cl00941 387092005731 rusticyanin; Region: rusti_cyanin; TIGR03095 387092005732 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 387092005733 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 387092005734 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 387092005735 Heme-binding domain of bacterial ethylbenzene dehydrogenase; Region: DOMON_EBDH; cd09623 387092005736 heme binding site [chemical binding]; other site 387092005737 beta subunit binding site [polypeptide binding]; other site 387092005738 putative heme-binding domain, Pirellula/Verrucomicrobium type; Region: CxxCH_TIGR02603 387092005739 Cytochrome c; Region: Cytochrom_C; pfam00034 387092005740 DMSO reductase family type II enzyme, iron-sulfur subunit; Region: DMSO_red_II_bet; TIGR03478 387092005741 4Fe-4S binding domain; Region: Fer4; cl02805 387092005742 Pseudogene. Similar to dimethylsulfide dehydrogenase alpha subunit precursor DdhA. This CDS appears to have a frameshift mutation following codon 676. 387092005743 Probable gene remnant. Similar to the C-terminal region of Rhodovulum sulfidophilum SH1 dimethylsulfide dehydrogenase alpha subunit precursor DdhA (910 aa). 387092005744 Probable gene remnant. Similar to the N-terminal region of Rhodovulum sulfidophilum SH1 dimethylsulfide dehydrogenase alpha subunit precursor DdhA (910 aa). 387092005745 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 387092005746 active site residue [active] 387092005747 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 387092005748 active site residue [active] 387092005749 Domain of unknown function DUF59; Region: DUF59; cl00941 387092005750 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 387092005751 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 387092005752 Walker A motif; other site 387092005753 Domain of unknown function DUF302; Region: DUF302; cl01364 387092005754 DsrE/DsrF-like family; Region: DrsE; cl00672 387092005755 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 387092005756 outer membrane porin, OprD family; Region: OprD; pfam03573 387092005757 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 387092005758 active site 387092005759 metal binding site [ion binding]; metal-binding site 387092005760 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 387092005761 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 387092005762 Cytochrome c [Energy production and conversion]; Region: COG3258 387092005763 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 387092005764 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 387092005765 Cytochrome c; Region: Cytochrom_C; cl11414 387092005766 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 387092005767 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 387092005768 dimer interface [polypeptide binding]; other site 387092005769 phosphorylation site [posttranslational modification] 387092005770 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 387092005771 ATP binding site [chemical binding]; other site 387092005772 Mg2+ binding site [ion binding]; other site 387092005773 G-X-G motif; other site 387092005774 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 387092005775 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 387092005776 active site 387092005777 phosphorylation site [posttranslational modification] 387092005778 intermolecular recognition site; other site 387092005779 dimerization interface [polypeptide binding]; other site 387092005780 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 387092005781 DNA binding site [nucleotide binding] 387092005782 Protein of unknown function (DUF3373); Region: DUF3373; pfam11853 387092005783 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 387092005784 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 387092005785 thiamine-phosphate pyrophosphorylase; Provisional; Region: PRK02615 387092005786 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 387092005787 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 387092005788 S-adenosylmethionine binding site [chemical binding]; other site 387092005789 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 387092005790 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u4_5s; cd10973 387092005791 putative active site [active] 387092005792 putative metal binding site [ion binding]; other site 387092005793 ribosome recycling factor; Reviewed; Region: frr; PRK00083 387092005794 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 387092005795 hinge region; other site 387092005796 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 387092005797 active site 387092005798 RDD family; Region: RDD; pfam06271 387092005799 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 387092005800 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 387092005801 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 387092005802 dimerization interface [polypeptide binding]; other site 387092005803 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 387092005804 dimer interface [polypeptide binding]; other site 387092005805 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 387092005806 putative CheW interface [polypeptide binding]; other site 387092005807 HTH domain; Region: HTH_11; pfam08279 387092005808 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 387092005809 dimer interface [polypeptide binding]; other site 387092005810 FMN binding site [chemical binding]; other site 387092005811 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 387092005812 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 387092005813 G1 box; other site 387092005814 putative GEF interaction site [polypeptide binding]; other site 387092005815 GTP/Mg2+ binding site [chemical binding]; other site 387092005816 Switch I region; other site 387092005817 G2 box; other site 387092005818 G3 box; other site 387092005819 Switch II region; other site 387092005820 G4 box; other site 387092005821 G5 box; other site 387092005822 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 387092005823 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 387092005824 phosphoglycolate phosphatase; Provisional; Region: PRK13222 387092005825 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 387092005826 motif II; other site 387092005827 deoxyguanosinetriphosphate triphosphohydrolase, putative; Region: dGTP_triPase; TIGR01353 387092005828 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 387092005829 Zn2+ binding site [ion binding]; other site 387092005830 Mg2+ binding site [ion binding]; other site 387092005831 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 387092005832 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 387092005833 putative active site [active] 387092005834 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 387092005835 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 387092005836 TPR motif; other site 387092005837 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 387092005838 active site 387092005839 putative DNA-binding cleft [nucleotide binding]; other site 387092005840 dimer interface [polypeptide binding]; other site